Methods of Assaying Neoplastic and Neoplasia-Related Cells and Uses Thereof

ABSTRACT

Methods are provided for assaying neoplastic cells and/or neoplasia-related cells. Aspects of the methods involve de-tecting heterogeneity, per cell programmed-death ligand 1 (PD-L1) expression, and/or proliferation of neoplasia and/or neoplasia-re-lated cells. Aspects of the methods include cytometrically assaying a labeled cell suspension to quantify per cell heterogeneity, per cell PD-L1 expression, proliferation, and/or other parameters to detect whether a neoplastic cell is present in the neoplasia sample. Aspects of the provided methods also include treating a subject based on the outcome of such an assay. In addition, kits that find use in practicing the subject methods are also provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to the filing date of the U.S. patentapplication Ser. No. 15/861,352, filed Jan. 3, 2018, which applicationis a continuation-in-part of International Application Serial No.PCT/US2017/050322, filed Sep. 6, 2017, which application claims priorityto the filing date of the U.S. Provisional Patent Application Ser. No.62/384,037, filed Sep. 6, 2016, the disclosures of which are hereinincorporated by reference.

INTRODUCTION

Cancer remains one of the leading causes of death globally, with anestimated 12.7 million annual cases around the world affecting bothsexes equally. This number is expected to increase to 21 million by2030.

The immune system is intimately involved with tumor development, playinga particularly decisive role during disease progression to metastasis.The impact of the immune system on a cancer is not strictly inhibitoryas the complex cross talk between immunity and cancer cells alsoenhances tumor growth. The involvement of the immune system in cancerprogression is now generally regarded as a hallmark of cancer. Thus, howthe immune system responds to a cancer determines the eventual outcome.Even in cases where a subject's immune system does mount a significantinitial response to a cancer, the cancer may still evade the destructiveelements of the immune response through various mechanisms including theexpression of immune check-point proteins to trigger immune suppression.Further mechanisms resulting in evasion of immune attack include theselection of tumor variants resistant to immune effectors (i.e.,“immuno-editing”) and progressive formation of an immune suppressiveenvironment within the tumor.

Immunotherapies seek to rationally redirect a subject's immune system toeffectively target the cancer and/or prevent immune evasion.

SUMMARY

Methods are provided for assaying neoplastic cells and/orneoplasia-related cells. Aspects of the methods involve detectingheterogeneity, per cell programmed-death ligand 1 (PD-L1) expression,and/or proliferation of neoplasia and/or neoplasia-related cells.Aspects of the methods include cytometrically assaying a labeled cellsuspension to quantify per cell heterogeneity, per cell PD-L1expression, proliferation, and/or other parameters to detect whether aneoplastic cell is present in the neoplasia sample. Aspects of theprovided methods also include treating a subject based on the outcome ofsuch an assay. In addition, kits that find use in practicing the subjectmethods are also provided.

BRIEF DESCRIPTION OF THE DRAWINGS

The invention is best understood from the following detailed descriptionwhen read in conjunction with the accompanying drawings. It isemphasized that, according to common practice, the various features ofthe drawings are not to-scale. On the contrary, the dimensions of thevarious features are arbitrarily expanded or reduced for clarity.Included in the drawings are the following figures.

FIG. 1 depicts clear cytometric separation of PD-L1 positive control andnegative control cells using PD-L1 labeling and flow cytometric analysisas described herein.

FIG. 2 depicts the linearity of PD-L1 positive cell detection in mixedsamples prepared with various percentages of PD-L1 positive cells spikedinto negative control samples.

FIG. 3 depicts MESF bead based standardization of PD-L1 fluorescence forper cell PD-L1 quantification as used in an embodiment as describedherein.

FIG. 4 depicts quantitative PD-L1 expression analysis of tumor andimmune cell subsets and validation of the specific detection of PD-L1expressing cells in patient derived samples.

FIG. 5 provides Table 2.

FIG. 6 depicts the proliferation of lung tumor tissue immune cellinfiltrates assayed according to an embodiment described herein.

FIG. 7 depicts a loss of macrophages and an increase of non-T cells intumor tissue as assayed according to an embodiment described herein.

FIG. 8 depicts an increase in aneuploidy, as compared to diploidy, oflymphocytes present in tumor tissue as assayed according to anembodiment described herein.

FIG. 9 depicts PD-L1 expression as a function of DNA content as assayedaccording to an embodiment of the methods described herein.

FIG. 10 depicts PD-L1 expression as a function of lung tumorheterogeneity.

FIG. 11 depicts the correlation between the presence of circulatingtumor cells (CTCs) and tumor proliferation.

FIG. 12 depicts the correlation between the presence of circulatingtumor cells (CTCs) and tumor aneuploidy.

FIG. 13 depicts PD-L1 versus DNA content data obtained by flow cytometry(left) and circulating tumor cell (CTC) cell cytometry (right).

DETAILED DESCRIPTION

Methods are provided for assaying neoplastic cells and/orneoplasia-related cells. Aspects of the methods involve detectingheterogeneity, per cell programmed-death ligand 1 (PD-L1) expression,and/or proliferation of neoplasia and/or neoplasia-related cells.Aspects of the methods include cytometrically assaying a labeled cellsuspension to quantify per cell heterogeneity, per cell PD-L1expression, proliferation, and/or other parameters to detect whether aneoplastic cell is present in the neoplasia sample. Aspects of theprovided methods also include treating a subject based on the outcome ofsuch an assay. In addition, kits that find use in practicing the subjectmethods are also provided.

Before the present invention is described in greater detail, it is to beunderstood that this invention is not limited to particular embodimentsdescribed, as such may, of course, vary. It is also to be understoodthat the terminology used herein is for the purpose of describingparticular embodiments only, and is not intended to be limiting, sincethe scope of the present invention will be limited only by the appendedclaims.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimit of that range and any other stated or intervening value in thatstated range, is encompassed within the invention. The upper and lowerlimits of these smaller ranges may independently be included in thesmaller ranges and are also encompassed within the invention, subject toany specifically excluded limit in the stated range. Where the statedrange includes one or both of the limits, ranges excluding either orboth of those included limits are also included in the invention.

Certain ranges are presented herein with numerical values being precededby the term “about.” The term “about” is used herein to provide literalsupport for the exact number that it precedes, as well as a number thatis near to or approximately the number that the term precedes. Indetermining whether a number is near to or approximately a specificallyrecited number, the near or approximating unrecited number may be anumber which, in the context in which it is presented, provides thesubstantial equivalent of the specifically recited number.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although any methods andmaterials similar or equivalent to those described herein can also beused in the practice or testing of the present invention, representativeillustrative methods and materials are now described.

All publications and patents cited in this specification are hereinincorporated by reference as if each individual publication or patentwere specifically and individually indicated to be incorporated byreference and are incorporated herein by reference to disclose anddescribe the methods and/or materials in connection with which thepublications are cited. The citation of any publication is for itsdisclosure prior to the filing date and should not be construed as anadmission that the present invention is not entitled to antedate suchpublication by virtue of prior invention. Further, the dates ofpublication provided may be different from the actual publication dateswhich may need to be independently confirmed.

It is noted that, as used herein and in the appended claims, thesingular forms “a”, “an”, and “the” include plural referents unless thecontext clearly dictates otherwise. It is further noted that the claimsmay be drafted to exclude any optional element. As such, this statementis intended to serve as antecedent basis for use of such exclusiveterminology as “solely,” “only” and the like in connection with therecitation of claim elements, or use of a “negative” limitation.

As will be apparent to those of skill in the art upon reading thisdisclosure, each of the individual embodiments described and illustratedherein has discrete components and features which may be readilyseparated from or combined with the features of any of the other severalembodiments without departing from the scope or spirit of the presentinvention. Any recited method can be carried out in the order of eventsrecited or in any other order which is logically possible.

While the apparatus and method has or will be described for the sake ofgrammatical fluidity with functional explanations, it is to be expresslyunderstood that the claims, unless expressly formulated under 35 U.S.C.§ 112, are not to be construed as necessarily limited in any way by theconstruction of “means” or “steps” limitations, but are to be accordedthe full scope of the meaning and equivalents of the definition providedby the claims under the judicial doctrine of equivalents, and in thecase where the claims are expressly formulated under 35 U.S.C. § 112 areto be accorded full statutory equivalents under 35 U.S.C. § 112.

Methods

As summarized above, methods are provided for detecting neoplastic cellsand/or neoplasia-related cells. Neoplastic cells include cells of, orcells derived from, a neoplasia, such as a tumor. Neoplasia-relatedcells include non-neoplastic cells associated with a neoplasia such ascells that are spatially associated with a neoplasia such as e.g.,immune cells, such as tumor infiltrating lymphocytes. Neoplasia cellsinclude cells that may or may not be spatially associated with aneoplasia but are derived from the neoplasia, such as e.g., metastaticcells and/or circulating tumor cells derived from the neoplasia. Methodsof the present disclosure may include, in some instances, direct and/orindirect detection of such neoplastic cells and/or neoplasia-relatedcells.

A cell may by identified as a neoplastic cell using various criteria.For example, in some instances, a cell may be identified as neoplastic,or potentially neoplastic, based on observation of the cellular and/orsubcellular morphology of the cell alone or in the context of tissuesurrounding the cell. In some instances, a cell behavior may be anindication that a cell is neoplastic, such as but not limited to e.g.,proliferation, migration, etc. In some instances, markers, such as butnot limited to e.g., proliferation markers, cell surface markers, cancermarkers, etc., may be employed to identify a cell as neoplastic. In someinstances, assaying gene expression, e.g., expression of a cancermarker, expression of a mutated gene, overexpression, underexpression,etc., may indicate whether a cell is neoplastic.

Correspondingly, a cell may be identified as neoplasia-related accordingto various criteria. In some instances, a cell may be identified asneoplasia-related based on being spatially associated with a neoplasiabut not fulfilling the criteria of a neoplastic cell (i.e., the cell isnon-neoplastic). A cell may be identified as non-neoplastic according tovarious criteria including but not limited to e.g., morphology (e.g.,normal morphology), behavior (e.g., proliferatively normal), markerexpression (e.g., absence of cancer marker expression), etc. In someinstances, a cell may be identified as neoplasia-related based on beingspatially associated (i.e., near or within) a neoplasia and being anon-neoplastic cell type such as but not limited to e.g., an immune cell(e.g., a tumor infiltrating lymphocyte), a stromal cell, etc.

Methods of the present disclosure may involve detecting heterogeneity,per cell programmed-death ligand 1 (PD-L1) expression, and/orproliferation of neoplasia cells and/or neoplasia-related cells. In someinstances, such methods may include cytometrically assaying a labeledcell suspension to quantify per cell heterogeneity, per cell PD-L1expression, proliferation, and/or other parameters to detect whether aneoplastic cell is present in a sample and/or a subject based onanalyzing a sample obtained from a subject.

As summarized above, embodiments are directed to methods of detecting acell that expresses programmed-death ligand 1 (PD-L1) above apredetermined threshold. Cells in which PD-L1 expression may be detectedin the subject methods include, in various instances, neoplastic cellsand immune cells. Accordingly, in some instances a cell e.g., aneoplastic cell, detected in the subject methods will have a per cellexpression level of PD-L1 protein that exceeds a predeterminedthreshold.

By “per cell expression level of PD-L1” or “per cell expression ofPD-L1”, as used herein, is meant the quantity of PD-L1 molecules presenton the surface of a cell. Methods of the present disclosure includecytometrically assaying a cellular sample to quantify the per cellexpression of PD-L1 and subsequently detecting one or more cells in thesample that have a per cell expression level of PD-L1 protein thatexceeds the predetermined threshold. Various means of cytometricallyassaying a cellular sample, described in more detail below, may beemployed in the subject methods.ss

PD-L1 Expressing Cells

As summarized above, the present disclosure provides methods ofdetecting cells expressing PD-L1 above a predetermined threshold. PD-L1expression may be quantified on a per cell basis based on the level ofPD-L1 protein expression or the level of PD-L1 encoding transcript(i.e., mRNA) expression. In some instances, the subject methodquantifies only per cell PD-L1 protein expression and does not quantifyper cell PD-L1 transcript expression. In some instances, a combinedmethod of quantifying both PD-L1 protein levels and PD-L1 transcriptionlevels may be employed.

As described in more detail below, embodiments of the instant methodsmay include cytometrically assaying a cell suspension to detect a cellexpressing PD-L1 above a predetermined threshold. As used herein, theterm “cytometrically assaying” describes the measuring of cellularparameters on a cell-by-cell basis where such measuring allows for thedetection of individual cells that have, or the counting of a cellpopulation that shares, a certain cellular parameter or set ofparameters. One such parameter that is cytologically assayed in thesubject methods is per cell expression of PD-L1.

PD-L1 (also known as CD274) binds programmed cell death protein 1(PD-1), a protein encoded by the PDCD1 gene that is a cell surfacereceptor expressed on T-cells. PD-1 functions as an immune checkpoint bypreventing the activation of T-cells, which reduces autoimmunity andpromotes self-tolerance. PD-L1 has been found to be expressed on anumber of different cancer cell types. The presence of PD-L1 on a cancercell inhibits T cell activation, contributing to cancer cell immuneevasion. A number of cancer therapies are directed to preventing cancercell immune evasion by inhibiting the PD-1/PD-L1 interaction.

The present disclosure includes detecting neoplastic cells expressingPD-L1 above a predetermined threshold. Neoplastic cells having a percell PD-L1 expression level above a predetermined threshold may be morelikely to effectively evade the host immune system. Neoplastic cellshaving a per cell PD-L1 expression level above a predetermined thresholdmay be more likely to be affected by therapies directed at disruptingthe PD-1/PD-L1 interaction. In some instances, by effectivelyquantifying PD-L1 expression on the surface of a neoplastic cell anddetecting neoplastic cells that express PD-L1 above a threshold levelthe effectiveness of therapies targeting the PD-1/PD-L1 interaction maybe predicted.

The present disclosure includes methods of identifying whether aneoplasia in a subject is anti-PD-1/PD-L1 immunotherapy responsive. Asused herein, anti-PD-1/PD-L1 immunotherapy responsive generally refersto the responsiveness of a neoplasia to a treatment targeting theinteraction between PD-1 and PD-L1, including e.g., by using anantagonist to PD-1 and/or PD-L1. As such, a cell having a PD-L1expression level above a predetermined threshold may, in some instances,be referred to as an anti-PD-1/PD-L1 immunotherapy responsive cell. Aneoplasia having one or more anti-PD-1/PD-L1 immunotherapy responsivecells may, in some instances, be referred to as an anti-PD-1/PD-L1immunotherapy responsive neoplasia. The responsiveness of a cell or aneoplasia to an anti-PD-1/PD-L1 immunotherapy may be predicted ordetermined. For example, in some instances, a method that detects thepresence of a cell expressing PD-L1 above a predetermined threshold maybe predictive that the neoplasia from which the cell is derived isanti-PD-1/PD-L1 immunotherapy responsive. In some instances, e.g., thepresence of a cell expressing PD-L1 above a predetermined thresholdpositively identifies that the neoplasia from which the cell is derivedis anti-PD-1/PD-L1 immunotherapy responsive. The subject methods finduse in detecting cells having a level of PD-L1 expression above apredetermined threshold derived from various different neoplasms,described in more detail below.

Cells detected in the methods of the present disclosure will have alevel of PD-L1 expression above a predetermined threshold. As such, themethods of the instant disclosure include cytometrically quantifying percell expression levels of PD-L1 to identify cells expressing PD-L1protein and/or PD-L1 transcript above a predetermined threshold.Predetermined thresholds for PD-L1 expression useful in the instantdisclosure will vary depending on various factors include e.g., the celltype assayed (e.g., the type of neoplasm from which the cell isderived), other measured cellular parameters (e.g., cell cycleparameters, aneuploidy parameters, etc.), and whether PD-L1 protein ortranscript are detected. As described in more detail below, PD-L1expression is determined cytometrically where PD-L1 protein expressionmay be determined by a variety of protocols including, but not limitedto, contacting the cell with a labeled specific binding member thatbinds PD-L1 protein on the surface of the cell. In some instances, PD-L1expression is determined cytometrically where PD-L1 transcriptexpression may be determined by a variety of protocols including, butnot limited to, contacting the cell with a labeled specific bindingmember that binds PD-L1 transcripts within the cell.

In some instances, quantifying per cell PD-L1 expression may includecalibrating PD-L1 fluorescence of PD-L1 specific binding partner labeledcells to a reference standard. Depending on the context, a referencestandard may be cytometrically assayed in parallel, in series orsimultaneously with the assayed cells. For example, in some instances, areference standard may be cytometrically assayed to calibrate the assayfor quantification and then the label cell suspension sample may beassayed using the calibrated cytometric assay. In some instances, areference standard may be added to (i.e., spiked into) the label cellsuspension sample and the calibration based on the reference standardfor quantifying the per cell expression of the labeled cells may beperformed during cytometric analysis of cells. In some instances,calibration with a reference standard may be performed between or duringeach run of a labeled cell sample. In some instances, calibration with areference standard may be performed between or during each batch ofruns.

Any convenient reference standard for calibrating labeled cellfluorescence to per cell marker expression may be employed in the hereindescribed assays including but not limited to e.g., standardizedmicrospheres (i.e., beads), standardized control cells, standardizedfluorescent particles, and the like. In some instances, spectrallyequivalent microsphere standards, such as e.g., Molecules of EquivalentSoluble Fluorochrome (MESF) beads or Mean Equivalent Fluorochrome (MEFL)beads, may be used. Microsphere standards useful in quantitativecytometry will vary any will generally include microspheres labeled witha known amount of fluorophore bound per microsphere or microspheres willa known valency for binding fluorophore labeled molecules. Microspherestandards for quantitative cytometry simulate fluorescent dye attachmentto the cell membrane of target cells and allow for calibration ofcytometric assays, including e.g., flow cytometric assays or cellcytometric assays, for quantification.

For example, in some instances, microsphere standards for quantitativecytometry will include two or more populations, including e.g., 2populations, 3 populations, 4 populations, 5 populations, 6 populations,etc., of microspheres labeled with different amounts of a fluorophore.The fluorophore chosen will generally be the same as or equivalent to orcomparable with the fluorophore used in one or more of the labeledspecific binding members of the described methods. Useful fluorophoresin microsphere standards include but are not limited to e.g., AlexaFluor 488, Alexa Fluor 647, FITC, PE, Cy5, APC, etc. In some instances,two or more microsphere standards having different fluorophores may bemixed, e.g., where quantification of two or more differently labeledspecific binding members are used in a subject method. In someinstances, microsphere standards having different fluorophores are notmixed and different populations of microspheres having different amountsof a single type of fluorophore bound may be employed.

Microsphere standards may be directly conjugated to the fluorescentlabel or, in some instances, fluorescently labeled antibody may be boundto the microsphere standard. In some instances, a microsphere standardmay be non-fluorescent but “label-able”. Label-able microspherestandards will generally have a known antibody binding capacity allowingfor staining of the microsphere with a known amount of a user'santibody, including e.g., the same antibody used as a specific bindingmember in a herein described method. Label-able microsphere standardsmay, in some instances, be employed in conjunction with a pre-labeledmicrosphere standard allowing for determination of the fluorophore toprotein (FTP) ratio of the particular labeled specific binding memberemployed in the method and/or further calibration. Various differentmicrosphere standards, including e.g., fluorescently labeled microspherestandards and label-able microsphere standards, for quantitativecytometry that may find use in the herein described methods include butare not limited to e.g., those commercially available from BangsLaboratories, Inc. (Fishers, Ind.), BD Biosciences (San Jose, Calif.),and the like.

In some embodiments, the fluorescence of a labeled specific bindingmember and/or cells labeled with such may be calibrated to microspherestandards (e.g., by assessing the fluorescence of two or morepopulations of microspheres labeled with different amounts of afluorophore) to establish a standard curve. Following or during theestablishment of a standard curve a labeled cell suspension sample maybe assayed and per cell PD-L1 expression may be determined. Quantifiedper cell PD-L1 expression levels may be compared to a predeterminedthreshold, including e.g., a threshold established based on the numberof molecules of PD-L1 protein expressed per cell, a thresholdestablished based on background fluorescence, a threshold establishedbased on background expression (including e.g., per cell expression) ofPD-L1, and the like.

In some instances, a predetermined threshold for per cell PD-L1expression may be expressed as a number of molecules of the PD-L1protein per cell, including but not limited to e.g., a threshold of 10molecules per cell, a threshold of 20 molecules per cell, a threshold of30 molecules per cell, a threshold of 40 molecules per cell, a thresholdof 50 molecules per cell, a threshold of 60 molecules per cell, athreshold of 70 molecules per cell, a threshold of 80 molecules percell, a threshold of 90 molecules per cell, a threshold of 100 moleculesper cell, a threshold of 200 molecules per cell, a threshold of 300molecules per cell, a threshold of 400 molecules per cell, a thresholdof 500 molecules per cell, a threshold of 600 molecules per cell, athreshold of 700 molecules per cell, a threshold of 800 molecules percell, a threshold of 900 molecules per cell, a threshold of 1000molecules per cell, a threshold of 1100 molecules per cell, a thresholdof 1200 molecules per cell, a threshold of 1300 molecules per cell, athreshold of 1400 molecules per cell, a threshold of 1500 molecules percell, a threshold of 1600 molecules per cell, a threshold of 1700molecules per cell, a threshold of 1800 molecules per cell, a thresholdof 1900 molecules per cell, a threshold of 2000 molecules per cell, etc.

Accordingly, in some instances, a cell is detected as expressing PD-L1above a predetermined threshold if the cell is identified as having aper cell number of PD-L1 protein molecules expressed on the surface ofthe cell that is above one or more of the predetermined thresholdslisted above.

In some instances, the methods described herein detect a single cellhaving a level of PD-L1 expression above a predetermined threshold. Insome instances, the presence of a single detected cell having a level ofPD-L1 expression above a predetermined threshold is consideredsignificant. In some instances, the methods described herein may includea threshold of cells having a level of PD-L1 expression above apredetermined threshold for the detected cells to be consideredsignificant (i.e., a minimum size for the population of cells having alevel of PD-L1 expression above a predetermined threshold to beconsidered significant). Depending on the context, the size of thedetected population of cells expressing PD-L1 above the threshold willvary and may range from one cell to millions of cells, including but notlimited to e.g., one cell, one cell or more, 10 cells or more, 100 cellsor more, 1,000 cells or more, 10,000 cells or more, 100,000 cells ormore.

In some instances, the size of the detected population of cellsexpressing PD-L1 above the predetermined threshold may be expressed inrelative terms. For example, the size of the population may be expressedas a percentage of all the cells in the sample, a percentage of all thecells analyzed, a percentage of all of the cells of a particular typewithin the sample, a percentage of all of the cells of a particular typethat were analyzed, etc. In some instances, the size of the detectedpopulation may exceed 0.01% or more of the neoplastic cells in the cellsuspension sample, including but not limited to e.g., 0.1% or more, 1%or more, 10% or more, etc.

In some instances, in order to classify a cell, e.g., a neoplasia cell,as PD-L1 expressing or likely to be anti-PD-1/PD-L1 immunotherapyresponsive or detected as anti-PD-1/PD-L1 immunotherapy responsive thesize of the population of cells detected as expressing PD-L1 above apredetermined threshold must exceed a predetermined threshold. Asdescribed above, the threshold for the size of the detected population,e.g., for a neoplasia to be considered PD-L1 expressing, will vary basedon a number of factors and in some instances may be one cell. In someinstances, the threshold for the size of the detected population, e.g.,for a neoplasia to be considered PD-L1 expressing, the population mustexceed more than one cell including two cells or more including but notlimited to e.g., 0.01% or more of the neoplastic cells in the sample,0.1% or more of the neoplastic cells in the sample, 1% or more of theneoplastic cells of the sample, and the like.

Cytometric Assays

As summarized above, methods of the present disclosure includecytometrically assaying a labeled cell suspension. Various methods ofcytometrically assaying a labeled cell suspension may find use in theherein described methods including but not limited to e.g., flowcytometrically assaying using a flow cytometer, cell cytometricallyassaying a labeled cell suspension, e.g., by using a cell cytometer, andthe like. Labeled cell suspension samples may be assayed for per cellPD-L1 expression. In some cases, additional cellular parameters, assayedcytometrically, may also find use in detecting neoplastic cells of theinstant disclosure. Accordingly, various methods of cytometricallyassaying a labeled cell suspension to measure various cellularparameters may be employed.

In some embodiments, cytometrically assaying a cellular sample may beperformed using flow cytometry. Flow cytometry is a methodology usingmulti-parameter data for identifying and distinguishing betweendifferent particle (e.g., cell) types i.e., particles that vary from oneanother in terms of label (wavelength, intensity), size, etc., in afluid medium. In flow cytometrically analyzing a sample, an aliquot ofthe sample is first introduced into the flow path of the flow cytometer.When in the flow path, the cells in the sample are passed substantiallyone at a time through one or more sensing regions, where each of thecells is exposed separately and individually to a source of light at asingle wavelength (or in some instances two or more distinct sources oflight) and measurements of cellular parameters, e.g., light scatterparameters, and/or marker parameters, e.g., fluorescent emissions, asdesired, are separately recorded for each cell. The data recorded foreach cell is analyzed in real time or stored in a data storage andanalysis means, such as a computer, for later analysis, as desired.

In flow cytometry-based methods, the cells are passed, in suspension,substantially one at a time in a flow path through one or more sensingregions where in each region each cell is illuminated by an energysource. The energy source may include an illuminator that emits light ofa single wavelength, such as that provided by a laser (e.g., He/Ne orargon) or a mercury arc lamp or an LED with appropriate filters. Forexample, light at 488 nm may be used as a wavelength of emission in aflow cytometer having a single sensing region. For flow cytometers thatemit light at two distinct wavelengths, additional wavelengths ofemission light may be employed, where specific wavelengths of interestinclude, but are not limited to: 405 nm, 535 nm, 561 nm, 635 nm, 642 nm,and the like. Following excitation of a labeled specific binding memberbound to a polypeptide by an energy source, the excited label emitsfluorescence and the quantitative level of the polypeptide on each cellmay be detected, by one or more fluorescence detectors, as it passesthrough the one or more sensing regions.

In flow cytometry, in addition to detecting fluorescent light emittedfrom cells labeled with fluorescent markers, detectors, e.g., lightcollectors, such as photomultiplier tubes (or “PMT”), an avalanchephotodiode (APD), etc., are also used to record light that passesthrough each cell (generally referred to as forward light scatter),light that is reflected orthogonal to the direction of the flow of thecells through the sensing region (generally referred to as orthogonal orside light scatter) as the cells pass through the sensing region and isilluminated by the energy source. Each type of data that is obtained,e.g., forward light scatter (or FSC), orthogonal light scatter (SSC),and fluorescence emissions (FL1, FL2, etc.), comprise a separateparameter for each cell (or each “event”).

Flow cytometers may further include one or more electrical detectors. Incertain embodiments, an electrical detector may be employed fordetecting a disturbance caused by a particle or cell passing through anelectrical field propagated across an aperture in the path of theparticles/cells. Such flow cytometers having electrical detectors willcontain a corresponding electrical energy emitting source thatpropagates an electrical field across the flow path or an aperturethrough which cells are directed. Any convenient electrical field and/orcombination of fields with appropriate detector(s) may be used for thedetection and/or measurement of particles (or cells) passing through thefield including but not limited to, e.g., a direct current electricalfield, alternating current electrical field, a radio-frequency field,and the like.

Flow cytometers further include data acquisition, analysis and recordingmeans, such as a computer, wherein multiple data channels record datafrom each detector for each cell as it passes through the sensingregion. The purpose of the analysis system is to classify and countcells wherein each cell presents itself as a set of digitized parametervalues and to accumulate data for the sample as a whole.

A particular cell subpopulation of interest may be analyzed by “gating”based on the data collected for the entire population. To select anappropriate gate, the data is plotted so as to obtain appropriateseparation of subpopulations, e.g., by adjusting the configuration ofthe instrument, including e.g., excitation parameters, collectionparameters, compensation parameters, etc. In some instances, thisprocedure is done by plotting forward light scatter (FSC) vs. side(i.e., orthogonal) light scatter (SSC) on a two dimensional dot plot.The flow cytometer operator then selects the desired subpopulation ofcells (i.e., those cells within the gate) and excludes cells which arenot within the gate. Where desired, the operator may select the gate bydrawing a line around the desired subpopulation using a cursor on acomputer screen. Only those cells within the gate are then furtheranalyzed by plotting the other parameters for these cells, such asfluorescence.

Any flow cytometer that is capable of obtaining fluorescence data, e.g.,as described above, may be employed. Useful flow cytometers includethose utilizing various different means of flowing a cell through thesensing region substantially one at a time including, e.g., a flow cell,a microfluidics chip, etc. Non-limiting examples of flow cytometersystems of interest are those available from commercial suppliersincluding but not limited to, e.g., Becton-Dickenson (Franklin Lakes,N.J.), Life Technologies (Grand Island, N.Y.), Acea Biosciences (SanDiego, Calif.), Beckman-Coulter, Inc. (Indianapolis, Ind.), Bio-RadLaboratories, Inc. (Hercules, Calif.), Cytonome, Inc. (Boston, Mass.),Amnis Corporation (Seattle, Wash.), EMD Millipore (Billerica, Mass.),Sony Biotechnology, Inc. (San Jose, Calif.), Stratedigm Corporation (SanJose, Calif.), Union Biometrica, Inc. (Holliston, Mass.), CytekDevelopment (Fremont, Calif.), Propel Labs, Inc. (Fort Collins, Colo.),Orflow Technologies (Ketchum, Id.), handyem inc. (Québec, Canada),Sysmex Corporation (Kobe, Japan), Partec Japan, Inc. (Tsuchiura, Japan),Bay bioscience (Kobe, Japan), Furukawa Electric Co. Ltd. (Tokyo, Japan),On-chip Biotechnologies Co., Ltd (Tokyo, Japan), Apogee Flow SystemsLtd. (Hertfordshire, United Kingdom), and the like.

In some embodiments, cytometrically assaying a cellular sample may beperformed using a cell cytometer. As used herein, the term “cellcytometer” (also referred to as an “imaging cytometer” or “automatedimaging cytometer”) generally refers to an automated or semi-automatedcell imaging device capable of imaging cells deposited on or in animaging vessel to collect data on all or most of the cells of a sample.In cell cytometry, imaging may be performed according to a variety ofdifferent methods. In some instances, a cell cytometer may collect awidefield image at low magnification (e.g., 5×, 10×, etc.) of the cellspresent on or in an imaging vessel to identify the location of the cellsand/or screen the cells for a particular parameter (e.g., size, shape,color, fluorescence, etc.). After identifying the location of the cellsa cell cytometer may proceed to collect higher magnification (e.g., 20×,40×, 60×, 100×, etc.) images of all or a portion of the identifiedcells, e.g., in a targeted manner.

In other instances, a cell cytometer may image cells present on or in animaging vessel by scanning the imaging vessel. Scanning may be performedat low or high magnification. In some instances, scanning is performedat high magnification to capture images of all or most of the cells. Insome instances, scanning is performed at low magnification to identifythe location of the cells on or in the imaging vessel. After identifyingthe location of the cells a cell cytometer may proceed to collect highermagnification images of all or a portion of the identified cells, e.g.,in a targeted manner, or may rescan the located cells at highmagnification.

The imaging vessels used in cell cytometer systems will vary. In someinstances, commonly used laboratory imaging devices such as e.g.,microscope slides, may serve as an imaging vessel in a cell cytometersystem. In some instances, a cell cytometer imaging vessel may bespecifically designed for use with a particular cell cytometer. Usefulimaging vessels include but are not limited to e.g., slides (e.g.,microscope slides), dishes (e.g., glass bottom imaging dishes), plates(e.g., multi-well imaging plates), etc. Imaging vessels will generallyhave optical properties amendable to microscopy, e.g., optical clarity,in at least a portion of the vessel. Imaging vessels may or may not haveindividual compartments. For example, a microscope slide utilized as animaging vessel does not generally have individual compartments and cellsdeposited on a slide may be spread about the surface of the slide.Alternatively, a multi-well imaging plate utilized as an imaging vesseldoes have individual compartments (i.e., wells) into which one or morecells may be deposited.

Cell cytometers include an imaging component such as, e.g., an automatedmicroscope. The imaging component of a cell cytometer may include one ormore objectives of various magnification power (e.g., 5×, 10×, 20×, 40×60×, 100×, etc.) for collecting light transmitted, reflected or emittedfrom the object (e.g., cell) being imaged. Light collected by theobjective will generally be processed through one or more dichroicmirrors, filters or lenses before being directed to an image capturedevice.

Suitable image capturing devices may include one or more digital cameras(including color and monochrome cameras) capable of capturing a digitalimage and a means of storing the digital image and/or transferring theimage to attached image processing circuitry or to an attached storagedevice for later transfer to image processing circuitry. Suitabledigital color cameras will vary and will generally include any digitalcamera (e.g., with one or more CCD or CMOS sensors). Suitable digitalcameras include but are not limited to e.g., custom built digitalcameras, consumer grade digital color cameras (e.g., consumer gradedigital color cameras converted for microscopic use) and those digitalmicroscopy color cameras commercially available from variousmanufactures including but not limited to e.g., Dino-Eye, Dino-Lite,Jenoptik ProgRes, KoPa, Leica, Motic, Olympus, Omano, OptixCam,PixelLINK, Zeiss, etc.

Cell cytometers further include data acquisition, analysis and recordingmeans, such as a computer, wherein one or more data channels record datafrom one or more image capture devices for each cell or most of thecells of the imaging vessel. The purpose of the analysis system is toclassify and count cells wherein each cell presents itself as a set ofdigitized parameter values and to accumulate data for the sample as awhole. In some cases, cell cytometers record images of each cell and maybe connected to a user interface where such images may be reviewed by auser of the device.

Cell cytometer based methods for detecting cells expressing a particularpolypeptide may include contacting the cells of a sample with afluorescent labeled specific binding member and detecting fluorescentlylabeled cells by imaging using the cell cytometer. As described in moredetail elsewhere herein, the fluorescence of each labeled cell may becytometrically quantified to identify the per cell expression of aparticular polypeptide, e.g., to detect whether a cell expresses thepolypeptide above a predetermined threshold.

Any cell cytometer that is capable of obtaining fluorescence data, e.g.,as described above, may be employed. Useful cell cytometers includethose utilizing various different means of automated cell cytometricimaging to analyze all or most of the cells of a sample. Non-limitingexamples of cell cytometer systems of interest are those available fromcommercial suppliers including but not limited to, e.g., NexcelomBioscience LLC (Lawrence, Mass.), Molecular Devices, LLC (Sunnyvale,Calif.), Thorlabs Inc. (Newton, N.J.), TTP Labtech Ltd. (UnitedKingdom), and the like.

Methods of the instant disclosure include cytometrically quantifying percell expression levels of particular polypeptides to identify cellsexpressing the polypeptide above a predetermined threshold. Methods ofthe instant disclosure may include cytometrically quantifying per cellPD-L1 expression to identify one or more cells expressing PD-L1 above apredetermined threshold. However, the levels of other markers besidesPD-L1 may also be assessed in the herein described methods includinge.g., cell cycle associated expression products (e.g., cell cycleassociated RNAs, cell cycle associated polypeptides, etc.),immune-related expression products (e.g., immune-related RNAs,immune-related polypeptides, etc.), DNA content, etc. Detection of cellshaving a level of a biomarker, e.g., above or below a predeterminedthreshold, or not having such other markers may serve to identifyfurther cell parameters useful in the herein described methods.

Predetermined thresholds may find use in identifying cells based ontheir expression of a particular polypeptide, as described above, orother cellular parameters including but not limited to e.g., cell cyclemarkers, aneuploidy markers, and the like.

Predetermined thresholds for polypeptide expression useful in theinstant disclosure will vary depending on the polypeptide detected andthe particular context. In some instances, a predetermined threshold forper cell polypeptide expression may be expressed as a number ofmolecules of the polypeptide per cell, including but not limited toe.g., a threshold of 10 molecules per cell, a threshold of 20 moleculesper cell, a threshold of 30 molecules per cell, a threshold of 40molecules per cell, a threshold of 50 molecules per cell, a threshold of60 molecules per cell, a threshold of 70 molecules per cell, a thresholdof 80 molecules per cell, a threshold of 90 molecules per cell, athreshold of 100 molecules per cell, a threshold of 200 molecules percell, a threshold of 300 molecules per cell, a threshold of 400molecules per cell, a threshold of 500 molecules per cell, a thresholdof 600 molecules per cell, a threshold of 700 molecules per cell, athreshold of 800 molecules per cell, a threshold of 900 molecules percell, a threshold of 1000 molecules per cell, a threshold of 1100molecules per cell, a threshold of 1200 molecules per cell, a thresholdof 1300 molecules per cell, a threshold of 1400 molecules per cell, athreshold of 1500 molecules per cell, a threshold of 1600 molecules percell, a threshold of 1700 molecules per cell, a threshold of 1800molecules per cell, a threshold of 1900 molecules per cell, a thresholdof 2000 molecules per cell, etc.

In other instances, a predetermined threshold may be a relative level ofa marker. Relative levels of a marker may be determined by a variety ofmeans including e.g., determined by making a comparison of the levels ofexpression of a marker in two separate populations of cells known todiffer in their level of the subject marker. For example, a first cellpopulation known to have a high level of Marker X is measured, e.g., ona cytometer, and compared to a second cell population, known to have alow level of Marker X and the comparison is used to determine athreshold level that may be used to categorize cells as either having alow or a high level of Marker X.

Relative levels of a marker may be determined by making a comparison ofthe levels of marker within a population of cells, e.g., a population ofcells of unknown levels of Marker X or a population of cells suspectedof containing subpopulations of cells having different levels of MarkerX. For example, the level of Marker X is measured on a cytometer of atleast a sufficient number of cells such that the measurements may beplotted, e.g., on a histogram, and separation between two or moresubpopulations of cells is revealed based on individual cell levels ofMarker X. Accordingly, the cytometer operator may then determine athreshold level between the subpopulations that may be used tocategorize cells as belonging to a particular subpopulation, e.g., asubpopulation having a low level of Marker X or a subpopulation havinghigh level of Marker X.

In some instances, a threshold may be based on the limit of detection ofthe cytometer. For example, cells of a population of cells may beidentified as having a particular marker (i.e., being positive for aparticular marker) if the cells have any detectable level of aparticular marker. Likewise, cells of a population of cells may beidentified as not having a particular marker (i.e., being negative for aparticular marker) if the cells do not have a detectable level of aparticular marker. Accordingly, the detection level of the cytometer maybe used to determine the marker threshold, as desired.

In some instances, a threshold may be based on previously determinedmarker levels, e.g., from previously performed control experiments orpreviously acquired reference expression levels. For example, markerlevels determined in previously analyzed samples may be used todetermine marker threshold levels. In some instances, marker levelsexpected of cells obtained from healthy subjects may be used todetermine normal marker levels such that a marker threshold that isrepresentative of the normal marker range may be determined. In suchinstances, marker expression outside, i.e., above or below, the normalmarker range is considered to be either above or below the particularmarker threshold. In some instances, use of such previously determinedmarker levels or previously determined threshold levels allows analysisof cells and the identification of cellular subpopulations in theabsence of a control or reference cellular sample.

As noted above, methods of the instant disclosure may include assayingcell cycle parameters. Useful cell cycle parameters include but are notlimited to e.g., proliferation, cell cycle phase (G₁, G₂, M,G₂-M, S, G₀,post G₁, and the like), etc. Cell cycle parameters may be assessed on aper cell basis, including e.g., identifying whether a cell isproliferative, identifying the cell cycle phase of a cell, etc. Anyconvenient means of determining a cell cycle parameter of a cell may beemployed in the subject methods. In some instances, a method may notonly quantify a particular cell type but also determine whether thequantified cell type is proliferative including e.g., the number orpercent of proliferative cells within the quantified cell type. In someinstances, a method may not only quantify an immune cell type but alsodetermine whether the quantified immune cell type is proliferativeincluding e.g., the number or percent of proliferative immune cellswithin the quantified immune cell type. In some instances, a method maydetermine whether proliferative tumor infiltrating lymphocytes arepresent and/or the quantity thereof. In some instances, a method maydetermine whether proliferative CD4+ cells are present and/or thequantity thereof. In some instances, a method may determine whetherproliferative CD8+ cells are present and/or the quantity thereof. Insome instances, a method may determine the ratio of CD4/CD8 cells andwhether the proliferative CD4 and/or CD8 cells are proliferative and/orthe quantity thereof.

In some instances, assaying the cell cycle of a cell may includedetermining the DNA content of the cell (i.e., the per cell DNAcontent). Various methods may be employed for assaying the cell cycle ofa cell by determining the per cell DNA content. In some instances, a DNAlabeling reagent (e.g., a nucleic acid dye or stain that containsintrinsic fluorescence) may be employed to label the DNA of the cell andthe amount of DNA may be quantified based on the measuring the intensityof the label. Depending on the method of cytometry employed in themethod, DNA content may be used to assess cell cycle in various ways. Inone embodiment, e.g., regardless of the type of cytometry employed(e.g., flow cytometry, cell cytometry, etc.), the fluorescent intensityof cells labeled with a DNA labeling reagent may analyzed on thecytometer and plotted on a histogram. From the histogram the relativeamount of DNA content may be determined for each cell allowing for theidentification of the cell cycle phase of each cell. In some instances,such a histogram may represent a cytometric cell cycle profile, alsoreferred to as a cytometric DNA profile.

In some instances, assaying the cell cycle of a cell may includeassaying an expressed cell cycle marker (also referred to as a cellcycle biomarker). Expressed cell cycle markers, as used herein, refer tothose cellular markers (e.g., cell surface markers and intracellularmarkers) that are specifically expressed or absent during one or moreparticular phases of the cell cycle. Accordingly a labeled bindingmember specific for an expressed cell cycle marker include to thosespecific binding members that bind components of the cell cyclemachinery of the cell. Cell cycle biomarkers may be useful, in someinstances, in determining the cell cycle phase of or determining whetheror not a cell is proliferative. Cell cycle biomarkers useful in themethods described herein will vary depending on the particular assayand/or the particular cell type and/or cell population to be detected.In some instances, cell cycle biomarkers that may find use in themethods described herein include but are not limited to, e.g., Ki67,cyclin D1, cyclin E, phosphorylated histone H3, and the like.

Expressed cell cycle markers may be detected in various ways. Forexample, an expressed cell cycle biomarker may be detected at theprotein level, e.g., through the use of a labeled specific bindingmember specific for the cell cycle biomarker protein. In some instances,an expressed cell cycle biomarker may be detected at the RNA level,e.g., through the use of a labeled specific binding member specific forthe cell cycle biomarker RNA.

As noted above, methods of the instant disclosure may include assayinganeuploidy. Any convenient method of measuring aneuploidy cytometricallymay be employed in the subject methods. In some instances, a cell may beidentified as aneuploid based on the measured DNA content of the cellwhere an aneuploid cell will generally have an abnormally high level ofDNA content representing duplication of all or a portion of the cell'sgenome. Similar methods to those described above for assessing DNAcontent in regards to cell cycle assessments may be employed fordetecting aneuploidy. In some instances, relative DNA content greaterthan or equal to a threshold DNA content value for a normal cell mayindicate that the cell is aneuploid where the threshold may be greaterthan or equal to (≥) 1.05 times the DNA content of a normal cellincluding but not limited to, e.g., ≥1.06 times, ≥1.07 times, ≥1.08times, ≥1.09 times, ≥1.10 times, ≥1.11 times, ≥1.12 times and ≥1.13times the DNA content of a normal cell.

In some instances, chromosome specific probes or gene specific probesmay be employed to assess aneuploidy. For example, fluorescent in situhybridization (FISH) using gene specific or chromosome specific probesmay be employed to determine the overall ploidy of a cell or to detectthe duplication of a particular gene or chromosome. For example, in adiploid organism, the presence of more than two probes for a specificgene or a specific chromosome may indicate that the subject cell isaneuploid.

Ploidy assessments (e.g., assessing the ploidy of a cell, includinge.g., whether a cell is aneuploid, diploid, etc.) may be employed in thesubject methods for various purposes. For example, in some instances, aploidy assessment may be employed to determine whether cells of apopulation are aneuploid or diploid, including e.g., to determinewhether a neoplastic cell is aneuploid or diploid, whether an immunecell is aneuploid or diploid, or the like. In some instances, a ploidyassessment may inform other characteristics of the sample and/or thesubject, e.g., by a relationship between the ploidy status of a detectedcell and other cell types that may be present in the subject. Forexample, in some instances, the identification of certain aneuploidcells may be indicative and/or predictive of the presence of aneoplastic cell type in a subject other than the detected aneuploid celltype, e.g., the presence of aneuploid immune cells in a tumor tissue ofthe subject may be indicative of the presence of circulating tumor cellsin the subject. In some instances, the presence of aneuploid immunecells in a lung tumor tissue may be indicative of the presence ofcirculating tumor cells in the subject.

Assessments of cellular parameters may be used in the subject methods todetect cells that have one or more characteristics detected by measuringthe described parameters. For example, in some instances, a detectedcell may be determined to be an aneuploid cell, e.g., based on one ormore assessed aneuploidy parameters of the cell. In some instances, adetected cell may be determined to be a proliferative cell, e.g., basedon one or more assessed cell cycle parameters of the cell. Cells may bedetected as having a combination of characteristics detected bymeasuring the described parameters. For example, a cell may bedetermined to be both proliferative and aneuploid. In addition, theabsence of a characteristic may also be used when detecting a particularcell including e.g., where the cell is not proliferative, where the cellis not aneuploid, etc. In some instances, a detected cell may have onecharacteristic and lack another, e.g., where the cell is proliferativebut not aneuploid, where the cell is aneuploid but no proliferative,etc. Any combination of the herein described parameters may find use inthe methods of the present disclosure.

As an example, useful combinations of determined parameters may includeper cell PD-L1 expression combined with ploidy status, including e.g.,where cells or a population of cells are detected that include per cellPD-L1 expression above a predetermined threshold and an aneuploid ploidystatus. Useful combinations may also include per cell PD-L1 expressioncombined with a DNA content or cell cycle determination. In someinstances, a heterogeneity index may be employed where such an index isa combination of parameters indicative of the heterogeneity of tumorcells. Useful heterogeneity indexes may include but are not limited toe.g., combinations of cell cycle and/or DNA content parameters combinedwith, e.g., measurements of cell complexity (e.g., side scatter, SSC)and/or PD-L1 expression measurements. In some instances, a heterogeneityindex will include or consist of a combination of cell cycle or DNAcontent determination, side scatter measurement and PD-L1quantification, including predetermined thresholds thereof.

In some instances, the methods of the instant disclosure may furtherinclude determining whether a subject cell is or is not an immune cell.Various methods may be employed for determining whether a subject cellis or is not an immune cell including e.g., through detecting thepresence or absence of one or more immune cell markers, e.g., throughcontacting the cell with a labeled specific binding member specific foran immune cell marker.

For example, in some instances, a non-immune neoplasia cell may bedetected based on expressing PD-L1 above a predetermined threshold andnot labeling with an immune cell specific binding member added to thecell suspension. Accordingly, in some instances, the method may furtherinclude determining that the identified cell is not an immune cell,e.g., by contacting the cell suspension with one or more labeledspecific binding members for immune cells.

Accordingly, in some instances, a cell and/or a population of cells maybe identified as being negative for a particular immune cell marker orhaving a level of expression of an immune cell marker that is below apredetermined threshold indicative that the cell is, in fact, not animmune cell or a particular type of immune cell. Useful immune cellmarkers, e.g., for identifying a PD-L1 expressing cell as not an immunecell include but are not limited to e.g., CD114, CD117, CD11a, CD11b,CD14, CD15, CD16, CD182, CD19, CD20, CD22, CD24, CD25, CD3, CD30, CD31,CD34, CD38, CD4, CD45, CD56, CD61, CD8, CD91, Foxp3, and the like.Accordingly, in some instances, a detected neoplasia cell may be furthercharacterized as lacking expression of or having expression of below apredetermined threshold of one or more immune cell markers, e.g., asdetected using an antibody to an immune cell marker including e.g.,those listed above.

In some instances, a cell may be assayed in the herein described methodsfor expression of a combination of immune cell markers including but notlimited to e.g., any combination of the here described markers. Forexample, in some instances, a PD-L1 expressing cell may be assayed forexpression of CD8 and CD45 and may be identified as not being an immunecell when the detected cell is negative for CD8 and CD45 or expressesCD8 and CD45 below a predetermined threshold indicative of the cell notbeing an immune cell.

In some instances, a cell may be detected based on expressing PD-L1above a predetermined threshold and labeling with an immune cellspecific binding member added to the cell suspension. Accordingly, insome instances, the method may further include determining that theidentified cell is an immune cell, e.g., by contacting the cellsuspension with one or more labeled specific binding members for immunecells.

Accordingly, in some instances, a cell and/or a population of cells maybe identified as being positive for a particular immune cell marker orhaving a level of expression of an immune cell marker that is above apredetermined threshold indicative that the cell is, in fact, an immunecell or a particular type of immune cell. Useful immune cell markers,e.g., for identifying a PD-L1 expressing cell as an immune cell includebut are not limited to e.g., CD114, CD117, CD11a, CD11b, CD14, CD15,CD16, CD182, CD19, CD20, CD22, CD24, CD25, CD3, CD30, CD31, CD34, CD38,CD4, CD45, CD56, CD61, CD8, CD91, Foxp3, and the like. Accordingly, insome instances, a detected cell may be further characterized as havingexpression of or having expression of above a predetermined threshold ofone or more immune cell markers, e.g., as detected using an antibody toan immune cell marker including e.g., those listed above.

In some instances, a cell may be assayed in the herein described methodsfor expression of a combination of immune cell markers including but notlimited to e.g., any combination of the here described markers. Forexample, in some instances, a PD-L1 expressing cell may be assayed forexpression of CD8 and CD45 and may be identified as being an immune cellwhen the detected cell is positive for CD8 and CD45 or expresses CD8 andCD45 above one or more predetermined thresholds indicative of the cellbeing an immune cell.

In some instances, the herein described methods may further includeassaying one or more markers for circulating tumor cells (CTC), e.g., inorder to determine if a detected PD-L1 expressing cell is a CTC. As usedherein, the term “CTC” generally refers to those neoplastic cells thathave sloughed off of a tumor (e.g., the edge of a tumor) and have beenswept away by the bloodstream or lymphatic system thus causing the CTCto circulate in the body. CTC makers include e.g., those markers used inidentifying CTCs in the blood stream including but not limited to e.g.,Epithelial cell adhesion molecule (EpCAM), cytokeratin 8, cytokeratin 18and cytokeratin 19. In some instances, CTCs may be further characterizedas being negative for one or more immune cell markers, including but notlimited to e.g., one or more of those immune cell markers describedherein. For example, in some instances, a detected CTC will be negativefor CD45.

In some instances, CTCs may be further identified and/or characterizedbased on the expression of one or more cancer antigens and/or one ormore cancer associated antigens. Non-limiting examples of cancerantigens include but are not limited to e.g., CD19, CD20, CD38, CD30,Her2/neu, ERBB2, CA125, MUC-1, prostate-specific membrane antigen(PSMA), CD44 surface adhesion molecule, mesothelin, carcinoembryonicantigen (CEA), epidermal growth factor receptor (EGFR), EGFRvIII,vascular endothelial growth factor receptor-2 (VEGFR2), high molecularweight-melanoma associated antigen (HMW-MAA), MAGE-A1, IL-13R-a2, GD2,and the like. Cancer-associated antigens also include, e.g., 4-1BB, 5T4,adenocarcinoma antigen, alpha-fetoprotein, BAFF, B-lymphoma cell, C242antigen, CA-125, carbonic anhydrase 9 (CA-IX), C-MET, CCR4, CD152, CD19,CD20, CD200, CD22, CD221, CD23 (IgE receptor), CD28, CD30 (TNFRSF8),CD33, CD4, CD40, CD44 v6, CD51, CD52, CD56, CD74, CD80, CEA, CN10888,CTLA-4, DRS, EGFR, EpCAM, CD3, FAP, fibronectin extra domain-B, folatereceptor 1, GD2, GD3 ganglioside, glycoprotein 75, GPNMB, HER2/neu, HGF,human scatter factor receptor kinase, IGF-1 receptor, IGF-I, IgG1,L1-CAM, IL-13, IL-6, insulin-like growth factor I receptor, integrinα5β1, integrin αvp3, MORAb-009, MS4A1, MUC1, mucin CanAg,N-glycolylneuraminic acid, NPC-1C, PDGF-R α, PDL192, phosphatidylserine,prostatic carcinoma cells, RANKL, RON, ROR1, SCH 900105, SDC1, SLAMF7,TAG-72, tenascin C, TGF beta 2, TGF-β, TRAIL-R1, TRAIL-R2, tumor antigenCTAA16.88, VEGF-A, VEGFR-1, VEGFR2, and vimentin.

In some instances, methods of the instant disclosure include detecting acell expressing PD-L1 above a predetermined threshold and furtheranalyzing the cell, e.g., based on detection of one or more of the CTCmarkers described above, to determine if the cell is a CTC. In someinstances, a CTC or a population of CTCs are collected from a sample(e.g., a blood sample of a subject) and the CTC or population of CTCsare assayed according to the methods described herein, e.g., todetermine if the CTC or CTCs of the population express PD-L1 above apredetermined threshold.

In some instances, methods of the instant disclosure may indirectlydetect and/or predict the presence of CTCs based on one or morecytometrically assayed parameters. For example, in some instances, thepresence or absence of CTCs may be indirectly detected or predictedbased on the measured ploidy status of cells of the sample, includinge.g., the measured ploidy status of neoplastic cells of the sample. Insome instances, the presence or absence of CTCs may be indirectlydetected or predicted based on the measured proliferative state of cellsof the sample, including e.g., the measured proliferative state ofneoplastic cells of the sample. The methods may include a step ofassigning an assayed sample as containing one or more CTCs, such that itis labeled or identified as a CTC containing sample. Depending on thesample employed, in some instances, a method of the present disclosuremay identify a sample as a CTC containing sample or a subject from whichthe subject was contained as a CTC containing subject. For example, insome instances, the methods may include a step of assigning a subject,from which an assayed sample was obtained, as having one or more CTCs,such that the subject is labeled or identified as a CTC containingsubject.

In such methods, the actual presence and/or amount of CTCs may or maynot be determined. Correspondingly, a sample assayed for indirectdetection of CTCs may or may not include CTCs. For example, where anassayed sample is obtained directly from a tissue that does not containCTCs or would not be expected to contain CTCs, the assay may identify asubject as having CTCs, e.g., based on the one or more cytometricallyassayed parameters of the cells of the sample, without CTCs actuallybeing present in the sample. As an example of this, a sample may beobtained from a non-hematological tissue (e.g., a non-hematologicaltumor) and the subject may be identified as containing CTCs, e.g., intheir blood system, based on cytometrically assayed parameters of thecells of the non-hematological tissue. In some embodiments, where anassayed sample is obtained directly from a tissue that may contain CTCs,the assay may identify a subject and/or the sample as having CTCs, e.g.,based on the one or more cytometrically assayed parameters of the cellsof the sample, without directly detecting the CTCs in the sample. As anexample of this, a sample may be obtained from a hematological tissue(e.g., blood) and the subject and/or the hematological sample may beidentified as containing CTCs or the subject may be identified ascontaining CTCs, e.g., in their blood system, based on cytometricallyassayed parameters of cells of the hematological tissue other than CTCs.

Methods of the present disclosure may thus include one or more steps ofassigning, labeling or identifying an assayed sample as containing oneor more cell populations, such assigning, labeling or identifying thesample as a CTC containing sample. Methods of the present disclosure mayalso include one or more steps of assigning, labeling or identifying asubject from which an assayed sample was obtained as containing one ormore cell populations, such assigning, labeling or identifying thesubject as a CTC containing subject. Such steps may be useful for avariety of purposes, including e.g., providing useful information as to:the type of treatment(s) that may be applied to a subject, the durationof treatment(s) that may be applied to a subject, the need for follow-upassays to be performed and/or when such follow-up may be performed, theneed to further test the sample (e.g., to directly assay for CTCs), andthe like. For example, in some instances, a method may indirectly detector predict the presence and/or prevalence of CTCs in a subject (e.g., byassigning a sample obtained from the subject as being a CTC containingsample), as determined by assaying a sample from the subject, withoutdirectly detecting and/or otherwise measuring CTCs in the sample or thesubject or a separate sample collected from the subject. Following sucha method, in some instances, the subject and/or the sample may belabeled as containing CTCs and further appropriate procedures, such asfurther testing and/or treatment may be identified and/or performed.

Methods of the instant disclosure include the detection of a cellexpressing PD-L1 above a predetermined threshold. In some instances, theinstant methods may encompass the detection of a plurality of cellsexpressing PD-L1 above the predetermined threshold. For example, in someinstances, the size of a population of cells expressing PD-L1 above thepredetermined threshold may be determined. Quantification of the size ofa population of cells expressing PD-L1 above the predetermined thresholdmay be measured cytometrically. For example, in some instances, a flowcytometer may be used to count the number of cells that express PD-L1above a predetermined threshold. In some instances, a cell cytometer maybe used to count the number of cells that express PD-L1 above apredetermined threshold. By counting the number of cells the size of thePD-L1 expressing population may be determined.

Samples

As summarized above, methods of the instant disclosure include detectingwhether a neoplastic cell that expresses PD-L1 above a predeterminedthreshold is present in a neoplasia sample. The herein described methodsare applicable to various neoplasia samples where a neoplasia sample mayinclude a sample of any neoplastic (i.e., abnormally growing) tissue orcell population or cell. Abnormal tissue growth may be determined by avariety of means including e.g., by comparing the growth of the subjecttissue to the growth of an appropriate normal or healthy tissue.Neoplasms include benign neoplasms, in situ neoplasms, malignantneoplasms, and neoplasms of uncertain or unknown behavior. Malignantneoplasms include cancer and accordingly the subject methods may includedetecting whether a cancer cell that expresses PD-L1 above apredetermined threshold is present in a cancer sample.

The methods described herein find use in detecting whether a neoplasticcell that expresses PD-L1 above a predetermined threshold is present ina variety of different neoplasia samples including e.g., samplesobtained from various cancers, including but not limited to e.g., AcuteLymphoblastic Leukemia (ALL), Acute Myeloid Leukemia (AML),Adrenocortical Carcinoma, AIDS-Related Cancers (e.g., Kaposi Sarcoma,Lymphoma, etc.), Anal Cancer, Appendix Cancer, Astrocytomas, AtypicalTeratoid/Rhabdoid Tumor, Basal Cell Carcinoma, Bile Duct Cancer(Extrahepatic), Bladder Cancer, Bone Cancer (e.g., Ewing Sarcoma,Osteosarcoma and Malignant Fibrous Histiocytoma, etc.), Brain StemGlioma, Brain Tumors (e.g., Astrocytomas, Central Nervous SystemEmbryonal Tumors, Central Nervous System Germ Cell Tumors,Craniopharyngioma, Ependymoma, etc.), Breast Cancer (e.g., female breastcancer, male breast cancer, childhood breast cancer, etc.), BronchialTumors, Burkitt Lymphoma, Carcinoid Tumor (e.g., Childhood,Gastrointestinal, etc.), Carcinoma of Unknown Primary, Cardiac (Heart)Tumors, Central Nervous System (e.g., Atypical Teratoid/Rhabdoid Tumor,Embryonal Tumors, Germ Cell Tumor, Lymphoma, etc.), Cervical Cancer,Childhood Cancers, Chordoma, Chronic Lymphocytic Leukemia (CLL), ChronicMyelogenous Leukemia (CML), Chronic Myeloproliferative Neoplasms, ColonCancer, Colorectal Cancer, Craniopharyngioma, Cutaneous T-Cell Lymphoma,Duct (e.g., Bile Duct, Extrahepatic, etc.), Ductal Carcinoma In Situ(DCIS), Embryonal Tumors, Endometrial Cancer, Ependymoma, EsophagealCancer, Esthesioneuroblastoma, Ewing Sarcoma, Extracranial Germ CellTumor, Extragonadal Germ Cell Tumor, Extrahepatic Bile Duct Cancer, EyeCancer (e.g., Intraocular Melanoma, Retinoblastoma, etc.), FibrousHistiocytoma of Bone (e.g., Malignant, Osteosarcoma, ect.), GallbladderCancer, Gastric (Stomach) Cancer, Gastrointestinal Carcinoid Tumor,Gastrointestinal Stromal Tumors (GIST), Germ Cell Tumor (e.g.,Extracranial, Extragonadal, Ovarian, Testicular, etc.), GestationalTrophoblastic Disease, Glioma, Hairy Cell Leukemia, Head and NeckCancer, Heart Cancer, Hepatocellular (Liver) Cancer, Histiocytosis(e.g., Langerhans Cell, etc.), Hodgkin Lymphoma, Hypopharyngeal Cancer,Intraocular Melanoma, Islet Cell Tumors (e.g., Pancreatic NeuroendocrineTumors, etc.), Kaposi Sarcoma, Kidney Cancer (e.g., Renal Cell, WilmsTumor, Childhood Kidney Tumors, etc.), Langerhans Cell Histiocytosis,Laryngeal Cancer, Leukemia (e.g., Acute Lymphoblastic (ALL), AcuteMyeloid (AML), Chronic Lymphocytic (CLL), Chronic Myelogenous (CML),Hairy Cell, etc.), Lip and Oral Cavity Cancer, Liver Cancer (Primary),Lobular Carcinoma In Situ (LCIS), Lung Cancer (e.g., Non-Small Cell,Small Cell, etc.), Lymphoma (e.g., AIDS-Related, Burkitt, CutaneousT-Cell, Hodgkin, Non-Hodgkin, Primary Central Nervous System (CNS),etc.), Macroglobulinemia (e.g., Waldenström, etc.), Male Breast Cancer,Malignant Fibrous Histiocytoma of Bone and Osteosarcoma, Melanoma,Merkel Cell Carcinoma, Mesothelioma, Metastatic Squamous Neck Cancerwith Occult Primary, Midline Tract Carcinoma Involving NUT Gene, MouthCancer, Multiple Endocrine Neoplasia Syndromes, Multiple Myeloma/PlasmaCell Neoplasm, Mycosis Fungoides, Myelodysplastic Syndromes,Myelodysplastic/Myeloproliferative Neoplasms, Myelogenous Leukemia(e.g., Chronic (CML), etc.), Myeloid Leukemia (e.g., Acute (AML), etc.),Myeloproliferative Neoplasms (e.g., Chronic, etc.), Nasal Cavity andParanasal Sinus Cancer, Nasopharyngeal Cancer, Neuroblastoma,Non-Hodgkin Lymphoma, Non-Small Cell Lung Cancer, Oral Cancer, OralCavity Cancer (e.g., Lip, etc.), Oropharyngeal Cancer, Osteosarcoma andMalignant Fibrous Histiocytoma of Bone, Ovarian Cancer (e.g.,Epithelial, Germ Cell Tumor, Low Malignant Potential Tumor, etc.),Pancreatic Cancer, Pancreatic Neuroendocrine Tumors (Islet Cell Tumors),Papillomatosis, Paraganglioma, Paranasal Sinus and Nasal Cavity Cancer,Parathyroid Cancer, Penile Cancer, Pharyngeal Cancer, Pheochromocytoma,Pituitary Tumor, Pleuropulmonary Blastoma, Primary Central NervousSystem (CNS) Lymphoma, Prostate Cancer, Rectal Cancer, Renal Cell(Kidney) Cancer, Renal Pelvis and Ureter, Transitional Cell Cancer,Retinoblastoma, Rhabdomyosarcoma, Salivary Gland Cancer, Sarcoma (e.g.,Ewing, Kaposi, Osteosarcoma, Rhabdomyosarcoma, Soft Tissue, Uterine,etc.), Sézary Syndrome, Skin Cancer (e.g., Childhood, Melanoma, MerkelCell Carcinoma, Nonmelanoma, etc.), Small Cell Lung Cancer, SmallIntestine Cancer, Soft Tissue Sarcoma, Squamous Cell Carcinoma, SquamousNeck Cancer (e.g., with Occult Primary, Metastatic, etc.), Stomach(Gastric) Cancer, T-Cell Lymphoma, Testicular Cancer, Throat Cancer,Thymoma and Thymic Carcinoma, Thyroid Cancer, Transitional Cell Cancerof the Renal Pelvis and Ureter, Ureter and Renal Pelvis Cancer, UrethralCancer, Uterine Cancer (e.g., Endometrial, etc.), Uterine Sarcoma,Vaginal Cancer, Vulvar Cancer, Waldenström Macroglobulinemia, WilmsTumor, and the like.

Samples useful in the herein described methods may be samples obtainedfrom a primary tumor, e.g., from a biopsy or surgical resection, or anon-tumor tissue. Non-tumor tissues may be assessed to for variousreasons including but not limited to for cancer surveillance. Forexample, in some instances a non-tumor tissue may be assayed to detect acell of a neoplasia expressing PD-L1 above a predetermined thresholdtherefore identifying the presence of the neoplasia. Both solid andfluid non-tumor samples may be assessed. Useful solid tissues that maybe assessed include but are not limited to e.g., tissue adjacent to anexisting cancer (e.g., skin tissue, lung tissue, breast tissue, etc.),lymph node tissue, etc. Useful fluid samples that may be assessedinclude essentially any bodily fluid sample including but are notlimited to e.g., blood samples, lymph fluid samples, etc.

Cancer and tumor tissues that may be assessed likewise include solid andliquid samples. For example, in the case of a hematopoietic cancer ablood sample or a bone marrow sample may be assessed. In some instances,the sample assessed according to the herein described methods is a solidtumor sample. Solid tumor samples may be obtained from a variety ofdifferent cancers, including e.g., any of those cancers listed above. Insome instances, a solid tumor sample may be a cancer of an epithelialtissue or an epithelial cancer.

Epithelial cancers include carcinomas. Non-limiting examples ofcarcinomas include acinar carcinoma , acinic cell carcinoma, acinouscarcinoma, adenocystic carcinoma , adenoid cystic carcinoma,adenosquamous carcinoma, adnexal carcinoma, adrenocortical carcinoma,alveolar carcinoma, ameloblastic carcinoma, apocrine carcinoma, basalcell carcinoma, bronchioloalveolar carcinoma, bronchogenic carcinoma,cholangiocellular carcinoma, chorionic carcinoma, clear cell carcinoma,colloid carcinoma, cribriform carcinoma, ductal carcinoma in situ,embryonal carcinoma, carcinoma en cuirasse, endometrioid carcinoma,epidermoid carcinoma, carcinoma ex mixed tumor, carcinoma ex pleomorphicadenoma, follicular carcinoma of thyroid gland, hepatocellularcarcinoma, carcinoma in si'tu, intraductal carcinoma, Hürthle cellcarcinoma, inflammatory carcinoma of the breast, large cell carcinoma,invasive lobular carcinoma, lobular carcinoma, lobular carcinoma in situ(LCIS), medullary carcinoma, meningeal carcinoma, Merkel cell carcinoma,mucinous carcinoma, mucoepidermoid carcinoma, nasopharyngeal carcinoma,non-small cell carcinoma , non-small cell lung carcinoma (NSCLC), oatcell carcinoma, papillary carcinoma, renal cell carcinoma, scirrhouscarcinoma, sebaceous carcinoma, carcinoma simplex, signet-ring cellcarcinoma, small cell carcinoma, small cell lung carcinoma, spindle cellcarcinoma, squamous cell carcinoma, terminal duct carcinoma,transitional cell carcinoma, tubular carcinoma, verrucous carcinoma, andthe like.

In some instances, the methods described herein find use in detectingwhether a neoplastic cell that expresses PD-L1 above a predeterminedthreshold is present in an epithelial tumor sample, including e.g., anepithelial lung cancer tumor, an epithelial breast cancer tumor, etc. Insome instances, the methods described herein find use in detectingwhether a neoplastic cell that expresses PD-L1 above a predeterminedthreshold is present in a non-small cell lung cancer (NSCLC) tumor. Insome instances, the epithelial tumor is a squamous cell carcinoma, anadenocarcinoma or an adenosquamous and the detected cell(s) includesquamous cell carcinoma cells, adenocarcinoma cells or adenosquamouscarcinoma cells.

In some instances, the herein described methods may be performed on aneoplasia sample that has been previously identified as PD-L1 positive.In some instances, the herein described methods may be performed on aneoplasia sample that are generally considered to or expected to expressPD-L1. Tumors that have been previously shown to express PD-L1 includebut are not limited to e.g., renal cell carcinoma (RCC), melanoma,ovarian cancer, NSCLC, etc. In some instances, a neoplasia sample mayhave been previously identified as PD-L1 positive byimmunohistochemistry (IHC). PD-L1 IHC as a companion diagnostic totherapy has been problematic in determining which patients will beresponsive to therapy. Issues with PD-L1 IHC include subjectivity of thereviewer, processing variability, differences in semi-quantitative cutoffs, variability in staining of tumor cells, staining of immune cells,staining of stromal cells, etc. In some instances, the methods describedherein may be utilized to validate the results of a previous PD-L1 IHCassay. In some instances, the herein described methods may be used inplace of a PD-L1 IHC assay as the method of the instant disclosure donot suffer from the issues associated with PD-L1 IHC.

Neoplasia samples containing neoplasia cells may be obtained using anyconvenient sample collection method, including but not limited to thosebiopsy methods for obtaining solid tissue biopsies and biopsy aspirates.In some instances, a sample containing neoplastic cells may be obtainedas part of a separate medical procedure performed for a purpose otherthan obtaining the sample, including but not limited to a surgicalprocedure. In other instances, a sample containing neoplastic cells maybe obtained independently, e.g., not as part of a separate medicalprocedure. Sample collection methods will vary and will depend upon,e.g., whether the collection is or is not performed as part of anadditional medical procedure, the particular type of sample to beobtained, the primary purpose for obtaining the sample and/or the methodby which the sample is to be processed and/or analyzed.

Samples used in the methods of the present disclosure may be collectedby any convenient means. In some instances, a neoplasia sample isprepared from a biopsy. Depending on the type of cancer and/or the typeof biopsy performed the sample may be prepared from a solid tissuebiopsy or a liquid biopsy.

In some instances, a sample may be prepared from a surgical biopsy. Anyconvenient and appropriate technique for surgical biopsy may be utilizedfor collection of a sample to be assessed according to the methodsdescribed herein including but not limited to, e.g., excisional biopsy,incisional biopsy, wire localization biopsy, and the like. In someinstances, a surgical biopsy may be obtained as a part of a surgicalprocedure which has a primary purpose other than obtaining the sample,e.g., including but not limited to tumor resection, mastectomy, lymphnode surgery, axillary lymph node dissection, sentinel lymph nodesurgery, and the like.

In some instances, a sample may be obtained by a needle biopsy. Anyconvenient and appropriate technique for needle biopsy may be utilizedfor collection of a sample to be analyzed according to the methodsdescribed herein including but not limited to, e.g., fine needleaspiration (FNA), core needle biopsy, stereotactic core biopsy, vacuumassisted biopsy, and the like.

FNA biopsy may be performed on both palpable and non-palpable lesionsand involves the introduction of a small-gauge needle, e.g., rangingfrom 18 to 25 gauge, into the mass or suspected area and the extractionof cellular material. Whether FNA is performed with or withoutco-imaging may vary and will depend on various factors including whetherthe lesion is palpable. In instances where FNA is performed withco-imaging the technique may be referred to as image-guided FNA and mayinclude but is not limited to radiological imaging techniques such asultrasound, computed tomography (CT), fluoroscopy, mammography, MRI, andthe like. FNA techniques, and variations thereof, useful in collectingsamples as described herein will vary and selection of specifictechniques will depend on various factors including but not limited to,e.g., the characteristics of the subject, the characteristics of theparticular detected lesion, the analysis procedure, etc. Variations ofsuch FNA techniques include but are not limited to, e.g., the open-endedneedle (i.e., the “French technique”), the negative pressure technique,imaging-guided FNA, and the like. As such, particular FNA techniques mayor may not include negative suction. For example, in the Frenchtechnique FNA short, rapid strokes within the lesion cause dislodgementof cells and allow effective collection within the needle via capillaryaction without the need for negative suction. In some instances, e.g.,when excess fluid (e.g., of a cystic lesion), a syringe with plungerremoved may be employed in collecting a sample by FNA. In someinstances, negative pressure may be utilized to draw the sample into asyringe. In some instances, a syringe holder or aspiration gun oraspiration handle may be used.

Core needle biopsy may be performed on both palpable and non-palpablelesions and involves the introduction of a hollow core needle into themass or suspected area and the extraction of cellular material. Whethercore needle biopsy is performed with or without co-imaging may vary andwill depend on various factors including whether the lesion is palpable.In instances where core needle biopsy is performed with co-imaging thetechnique may be referred to as image-guided core needle biopsy orstereotactic core needle biopsy and may include but is not limited toradiological imaging techniques such as ultrasound, computed tomography(CT), fluoroscopy, mammography, MRI, and the like. Variations of suchcore needle biopsy techniques include but are not limited to, e.g.,vacuum-assisted core biopsy, imaging-guided core biopsy, and the like.As such, particular core needle biopsy techniques may or may not includean incision made in the skin prior to insertion of the core biopsyneedle. For example, in the vacuum-assisted core biopsy a small cut ismade and a hollow probe is put through the cut and guided to the lesionsite and then a cylinder of tissue is then pulled into the probe byvacuum pressure. In general, a core needle biopsy obtains more tissuethan the described FNA technique.

In some instances, the term “needle biopsy” may generally refer anybiopsy which can be performed without anesthesia or may require onlylocal anesthesia and which are not considered surgical procedures. Insome instances, such biopsies may utilize devices other than “needles”such as, but not limited to, those devices that may be utilized toobtain a punch biopsy, e.g., a skin punch biopsy. Such devices includebut are not limited to, e.g., those devices used in the collection ofskin punch biopsies.

According to the particular biopsy method employed and depending on thespecifics of a particular subject and/or a subject's particular lesionone biopsy or multiple biopsies may be performed. For example, in someinstances, a single biopsy, e.g., a single FNA biopsy or a single coreneedle biopsy, may be performed to sufficiently sample a particularsubject or a particular subject's lesion. In other instances, multiplebiopsies, e.g., multiple FNA biopsies or multiple core needle biopsies,may be performed for the collection of a single sample or multiplesamples from a subject or a subject's lesion. In instances wheremultiple biopsies are collected the actual number of biopsies will varydepending on the particular subject and/or the particular lesion orlesions of the subject and, as such, may range from 2 to 10 or morebiopsies, including but not limited to, e.g., 2 biopsies, 3 biopsies, 4biopsies, 5 biopsies, 6 biopsies, 7 biopsies, 8 biopsies, 9 biopsies, 10biopsies, etc. Multiple biopsies may be collected in a co-timely manneror may be collected over a pre-determined period of time, e.g., as partof a surveillance protocol.

Neoplasia samples collected according to the methods described hereinmay be solid, semi-solid, or liquid samples. For example, in someinstances, by nature of the collection technique utilized, e.g.,techniques that cause the dissociation or aspiration of cells, thecollected sample may be a liquid sample upon collection. In otherinstances, by nature of the collection technique utilized, e.g.,surgical collection or core sample collection, the collected sample maybe a solid or semi-solid sample upon collection. In embodiments wherethe collected sample is a solid or semi-solid sample the cells of thesample may be dissociated to form a liquid sample following collection.Methods of dissociating solid and semi-solid tissue samples include butare not limited to mechanical dissociation, chemical dissociation,enzymatic dissociation, and combinations thereof.

In some instances, solid tumor samples may be subjected to mechanicalhomogenization. Any convenient method of mechanical homogenization mayfind use preparing a solid tissue sample for downstream steps includingbut not limited homogenization performed using a commercially availablehomogenization device including e.g., those available from IncellDx(Menlo Park, Calif.), such as e.g., those provided with the incellPREP(IncellDx, Inc) kit, Claremont BioSolutions (Upland, Calif.) includinge.g., the microHomogenizer (Claremont BioSolutions), the microDisruptor(Claremont BioSolutions), and the like. Mechanical homogenization may beperformed in any suitable solution, including e.g., a buffer. In someinstances, mechanical homogenization may be combined with chemical orenzymatic homogenization. In some instances, a fixation reagent is addedduring homogenization. In some instances, a fixation reagent is addedfollowing, including immediately following, homogenization. Fixationreagents, described in more detail below, that may be added followinghomogenization include but are not limited to e.g., the incellPREP(IncellDx, Inc). In some instances, a fixation solution may be acombination fixation/permeabilization reagent.

In some instances, the fixative used in preparing the labeled cellsuspension sample provides for the ability to cytometrically separatePD-L1 expressing cell from PD-L1 non-expressing cells, including but notlimited to e.g., to effectively cytometrically separate cells having aper cell PD-L1 expression level above a predetermined threshold fromthose having a per cell PD-L1 expression level below the predeterminedthreshold.

Upon collection or preparation of the sample, e.g., dissociation orhomogenization, the cells of the resultant liquid cell suspension of maybe fixed and/or permeabilized as desired. As such, aspects of themethods may include fixing the cells of the suspension by contacting thesample with a suitable fixation reagent. Fixation reagents of interestare those that fix the cells at a desired time-point. Any convenientfixation reagent may be employed, where suitable fixation reagentsinclude, but are not limited to mildly cross-linking agents. In someinstances, a mildly cross-linking agent may be a formaldehyde-basedfixative including but not limited to e.g., formaldehyde,paraformaldehyde, formaldehyde/acetone, IncelIFP (IncellDx, Inc), etc.In some instances, an alcohol-based fixative may be employed includingbut not limited to e.g., methanol/acetone, ethanol, etc. In someinstances, formaldehyde-based fixatives may be used at a finalconcentration of about 1 to 2%.

In some instances, the cells in the sample are permeabilized bycontacting the cells with a permeabilizing reagent. Permeabilizingreagents of interest are reagents that allow the labeled biomarkerprobes, e.g., as described in greater detail below, to access to theintracellular environment. Any convenient permeabilizing reagent may beemployed, where suitable reagents include, but are not limited to: milddetergents, such as Triton X-100, NP-40, saponin, etc.; methanol, andthe like.

Samples used in the methods of the present disclosure are assayedcytometrically. Accordingly, in some instances, a neoplasia sample maybe processed to generate a cell suspension suitable for cytometricassays. Processing to generate sample suitable for cytometric assays mayinclude e.g., any individual step or combination of the steps describedabove including e.g., homogenization, dissociation, fixation,permeabilization, etc. The amount of processing required will depend onvarious factors including the source of the sample where solid tissuesamples will generally require more processing that a liquid sample. Forexample, processing of a liquid sample, e.g., hematopoietic sample, maynot require homogenization or dissociation and thus may only requirefixation and/or permeabilization as desired.

The cells of a cell suspension sample will generally be labeled with oneor more labeled specific binding members. For example, methods of thepresent disclosure will generally include contacting a cell suspensionsample with a labeled specific binding member specific for PD-L1. Otherspecific binding members and other labeling reagents may find use in thesubject methods for labeling various aspects of a cell or cells of apopulation as described herein including but not limited to e.g., amaker (e.g., an immune cell marker), the nucleus of the cell, etc. Suchregents are described in more detail below.

Contacting, e.g., contacting a cell of a cell suspension with a specificbinding member may be carried out by any convenient and appropriatemeans. In some instances, a cell of a cell suspension may be contactedwith a specific binding member by adding an aliquot of the specificbinding member to the cell suspension. A contacted cell suspension maybe incubated and/or post-fixed as desired.

Reagents

A summarized above, the instant methods include the detection of a cellexpressing a per cell level of PD-L1 above a predetermined threshold andthus include various reagents useful in practicing the methods. Forexample, the instant methods generally include detecting a cellexpressing PD-L1 above a predetermined threshold by contacting the cellwith a labeled specific binding member reagent in order to allowcytometric assays to be performed.

In order to effectively cytometrically quantify the per cell level of aparticular polypeptide a direct correlation between the amount offluorescence measured from the labeled specific binding member and thenumber of polypeptides bound by the specific binding member may bedesired. In some instances, the amount of fluorescence emitted by thelabeled specific binding member is linearly correlated to the number ofpolypeptides bound by the labeled specific binding member. Generally,but not exclusively, a labeled specific binding member will bind onemolecule of the target polypeptide. As such, in some instances, theremay be a one-to-one correlation between the amount of fluorescencedetected from a plurality of labeled specific binding members bound topolypeptides on the surface of a cell and the number of the polypeptidesexpressed by the cell. Accordingly, in instances where per cellexpression of a polypeptide is quantified cytometrically, the labeledspecific binding members used may all uniformly have the same amount ofattached label such that each specific binding member emits essentiallythe same amount of fluorescence. For example, a labeled specific bindingmember may have a single attached label or a single fluorescent moiety.Alternatively, a labeled specific binding member may have a plurality ofattached label (e.g., 2 attached labels, 3 attached labels, 4 attachedlabels, etc.) or a plurality of fluorescent moieties (e.g., 2 moieties,3 moieties, 4 moieties, etc.) provided the plurality is the same foreach molecule of labeled specific binding member.

Specific binding agents of interest include antibody binding agents,proteins, peptides, haptens, nucleic acids, etc. The term “antibodybinding agent” as used herein includes polyclonal or monoclonalantibodies or fragments that are sufficient to bind to an analyte ofinterest. The antibody fragments can be, for example, monomeric Fabfragments, monomeric Fab′ fragments, or dimeric F(ab)′₂ fragments. Alsowithin the scope of the term “antibody binding agent” are moleculesproduced by antibody engineering, such as single-chain antibodymolecules (scFv) or humanized or chimeric antibodies produced frommonoclonal antibodies by replacement of the constant regions of theheavy and light chains to produce chimeric antibodies or replacement ofboth the constant regions and the framework portions of the variableregions to produce humanized antibodies. Nucleic acid binding agents ofinterest are nucleic acids that specifically bind or specificallyhybridize to biomarker nucleic acids in a cell. The length of thesenucleic acids may vary, so long as it is sufficient for theoligonucleotide to serve as a specific binding agent, and in someinstances ranges from 13 to 100 nt, such as 14 to 50 nt, e.g., 15 to 25nt, including but not limited to, e.g., 15 nt, 16 nt, 17 nt, 18 nt, 19nt, 20 nt, 21 nt, 22 nt, 23 nt, 24 nt, and 25 nt. The oligonucleotidesthat make up these nucleic acid binding agents may be DNA or RNA, or asynthetic analogue thereof, as desired.

As described above, the specific binding members described herein willgenerally be detectably labeled (i.e., have an attached detectablelabel, be bound by a detectable label, etc.). Therefore, in addition toa specific binding domain that specifically binds or specificallyhybridizes to the biomarker of interest, the specific binding agent mayfurther include or may be bound by or attached to a detectable label. Ofinterest as detectable labels are fluorescent dyes. Fluorescent dyes(fluorophores) can be selected from any of the many dyes suitable foruse in imaging applications (e.g., fluorescent microscopy) and cytometryapplications. A large number of dyes are commercially available from avariety of sources, such as, for example, Molecular Probes (Eugene,Oreg.) and Exciton (Dayton, Ohio). Examples of fluorophores of interestinclude, but are not limited to,4-acetamido-4′-isothiocyanatostilbene-2,2′disulfonic acid; acridine andderivatives such as acridine, acridine orange, acridine yellow, acridinered, and acridine isothiocyanate;5-(2′-aminoethyl)aminonaphthalene-1-sulfonic acid (EDANS);4-amino-N-[3-vinylsulfonyl)phenyl]naphthalimide-3,5 disulfonate (LuciferYellow VS); N-(4-anilino-1-naphthyl)maleimide; anthranilamide; BrilliantYellow; coumarin and derivatives such as coumarin,7-amino-4-methylcoumarin (AMC, Coumarin 120),7-amino-4-trifluoromethylcouluarin (Coumarin 151); cyanine andderivatives such as cyanosine, Cy3, Cy5, Cy5.5, and Cy7;4′,6-diaminidino-2-phenylindole (DAPI); 5′,5″-dibromopyrogallol-sulfonephthalein (Bromopyrogallol Red);7-diethylamino-3-(4′-isothiocyanatophenyl)-4-methylcoumarin;diethylaminocoumarin; diethylenetriamine pentaacetate;4,4′-diisothiocyanatodihydro-stilbene-2,2′-disulfonic acid;4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid;5-[dimethylamino]naphthalene-1-sulfonyl chloride (DNS, dansyl chloride);4-(4′-dimethylaminophenylazo)benzoic acid (DABCYL);4-dimethylaminophenylazophenyl-4′-isothiocyanate (DABITC); eosin andderivatives such as eosin and eosin isothiocyanate; erythrosin andderivatives such as erythrosin B and erythrosin isothiocyanate;ethidium; fluorescein and derivatives such as 5-carboxyfluorescein(FAM), 5-(4,6-dichlorotriazin-2-yl)aminofluorescein (DTAF),2′7′-dimethoxy-4′5′-dichloro-6-carboxyfluorescein (JOE), fluoresceinisothiocyanate (FITC), fluorescein chlorotriazinyl, naphthofluorescein,and QFITC (XRITC); fluorescamine; IR144; IR1446; Green FluorescentProtein (GFP); Reef Coral Fluorescent Protein (RCFP); Lissamine™;Lissamine rhodamine, Lucifer yellow; Malachite Green isothiocyanate;4-methylumbelliferone; ortho cresolphthalein; nitrotyrosine;pararosaniline; Nile Red; Oregon Green; Phenol Red; B-phycoerythrin;o-phthaldialdehyde; pyrene and derivatives such as pyrene, pyrenebutyrate and succinimidyl 1-pyrene butyrate; Reactive Red 4 (Cibacron™Brilliant Red 3B-A); rhodamine and derivatives such as6-carboxy-X-rhodamine (ROX), 6-carboxyrhodamine (R6G),4,7-dichlororhodamine lissamine, rhodamine B sulfonyl chloride,rhodamine (Rhod), rhodamine B, rhodamine 123, rhodamine Xisothiocyanate, sulforhodamine B, sulforhodamine 101, sulfonyl chloridederivative of sulforhodamine 101 (Texas Red),N,N,N′,N′-tetramethyl-6-carboxyrhodamine (TAMRA), tetramethyl rhodamine,and tetramethyl rhodamine isothiocyanate (TRITC); riboflavin; rosolicacid and terbium chelate derivatives; xanthene; or combinations thereof.Other fluorophores or combinations thereof known to those skilled in theart may also be used, for example those available from Molecular Probes(Eugene, Oreg.) and Exciton (Dayton, Ohio).

The methods of the present disclosure generally include the use of alabeled binding member specific of PD-L1 (i.e., a labeled PD-L1 specificbinding member) to label cells of the cell suspension thus generating alabeled cell suspension that may be cytometrically assayed. As describedabove, depending on the context, a labeled binding member specific forPD-L1 may specifically bind PD-L1 protein or may specifically bind PD-L1transcript.

In some instances, a labeled binding member specific for PD-L1 proteinmay specifically bind PD-L1 protein expressed on the surface of a cell.Human PD-L1 protein is a 290 amino acid polypeptide having a signalpeptide domain from residue 1 to about residue 18, an extracellulartopological domain from about residue 19 to about residue 238, atransmembrane domain from about residue 239 to about residue 259, and acytoplasmic topological domain from about residue 260 to 290. Theprimary isoform of human PD-L1 (programmed cell death 1 ligand 1 isoforma precursor NP_054862.1) has the following amino acid sequence:

(SEQ ID NO: 1) MRIFAVFIFMTYWHLLNAFTVTVPKDLWVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYNKINQRILVVDPVTSEHELTCQAEGYPKAEVIWTSSDHQVLSGKTTTTNSKREEKLFNVTSTLRINTTTNEIFYCTFRRLDPEENHTAELVIPELPLAHPPNERTHLVILGAILLCLGVALTFIFRLRKGRMMDVKKCGIQDTNSKKQSDTHLEET.Human PD-L1 also has a minor alternatively spliced isoform (programmedcell death 1 ligand 1 isoform b precursor NP_001254635.1) having thefollowing amino acid sequence:

(SEQ ID NO: 2) MRIFAVFIFMTYWHLLNAPYNKINQRILVVDPVTSEHELTCQAEGYPKAEVIWTSSDHQVLSGKTTTTNSKREEKLFNVTSTLRINTTTNEIFYCTFRRLDPEENHTAELVIPELPLAHPPNERTHLVILGAILLCLGVALTFIFRLRKGRMMDVKKCGIQDTNSKKQSDTHLEET.

Useful specific binding members specific for PD-L1 protein include butare not limited to antibodies, including but not limited to antibodiesthat bind one or both of the above human PD-L1 isoforms, the sequencesof which are provided. In some instances, anti-PD-L1 (i.e., anti-CD274)antibodies that are directly conjugated to a fluorophore may find use inthe described methods. Useful commercially available directly conjugatedanti-PD-L1 antibodies include but are not limited to e.g., those listedin Table 1 below.

TABLE 1 Commercial Supplier Antibody Fluor. Conjugation Acris AntibodiesAnti-human CD274/PDL1 FITC, PE GmbH Acris Antibodies Anti-mouseCD274/PDL1 FITC GmbH Novus Biologicals Goat Polyclonal Anti-Mouse B7-Allophycocyanin, H1/PD-L1/CD274 Antibody Fluorescein Novus BiologicalsMouse Monoclonal Anti-Human Phycoerythrin, Alexa Fluor B7-H1/PD-L1/CD274Antibody 700, Alexa Fluor 647, Alexa Fluor 594, Alexa Fluor 405,Allophycocyanin, PerCP, Phycoerythrin, Alexa Fluor 488, Alexa Fluor 350,Alexa Fluor 750 Novus Biologicals Rat Monoclonal Anti- PerCP, AlexaFluor 647, Human/Mouse B7-H1/PD- Alexa Fluor 594, DyLight L1/CD274Antibody 488, Alexa Fluor 405, Alexa Fluor 488, Alexa Fluor 647, AlexaFluor 700, DyLight 755, DyLight 350, PE, DyLight 680, Allophycocyanin,DyLight 405, DyLight 405LS R&D Systems Anti-Mouse B7-H1/PD-L1Allophycocyanin, Antibody Fluorescein, Alexa Fluor 594, Alexa Fluor 647R&D Systems Anti-Human B7-H1/PD-L1 Allophycocyanin, Alexa Antibody Fluor405, Alexa Fluor 488, Alexa Fluor 594, Alexa Fluor 647, Alexa Fluor 700,Phycoerythrin, PerCP Bio-Rad (Formerly Rat anti-mouse CD274 AntibodyFITC, Alexa Fluor 488, AbD Serotec) Alexa Fluor 647 Bio-Rad (FormerlyMouse anti-human CD274 Alexa Fluor 488, Alexa Fluor AbD Serotec)Antibody 647, FITC, RPE GeneTex Anti-human PD-L1 antibody FITC,Phycoerythrin (PE) GeneTex Anti-mouse PD-L1 antibody FITC TonboAnti-Mouse CD274 (PD-L1, B7- PE Biotechnologies H1) (10F.9G2) LifeSpanBioSciences Anti-human CD274/B7-H1/PD- FITC, PE L1 Antibody LifeSpanBioSciences Anti-human CD274/B7-H1/PD- FITC, RPE L1 Antibody (cloneMIH2) LifeSpan BioSciences Anti-human CD274/B7-H1/PD- FITC L1 Antibody(clone MIH6) LifeSpan BioSciences Anti-human CD274/B7-H1/PD- APC L1Antibody (aa19-238, clone 12K56) LifeSpan BioSciences Anti-humanCD274/B7-H1/PD- PE L1 Antibody (clone 27A2) LifeSpan BioSciencesAnti-human CD274/B7-H1/PD- FITC, RPE L1 Antibody (clone ANC6H1) LifeSpanBioSciences Anti-mouse CD274/B7-H1/PD- PE L1 Antibody (clone MIH5)LifeSpan BioSciences Anti-mouse CD274/B7-H1/PD- APC, FITC L1 Antibody(clone 10F.9G2) LifeSpan BioSciences Anti-mouse CD274/B7-H1/PD- APC, PEL1 Antibody (clone 29E.2A3) BioLegend Anti-mouse CD274 (B7-H1, PD- APC,Brilliant Violet 421, L1) Antibody PE/DZL594, Brilliant Violet 711, PE,PE/Cy7, Brilliant Violet 605 BioLegend Anti-human CD274 (B7-H1, PD- APC,Brilliant Violet 421, L1) Antibody Brilliant Violet 711, BrilliantViolet 605, APC, PE, PE/Cy7, PE/DZL594, PerCP/Cy5.5 GenWay Biotech, Inc.Anti-human CD274 Antibody FITC GenWay Biotech, Inc. Anti-mouse CD274Antibody FITC Abeam Anti-human PD-L1 antibody Phycoerythrin (MIH2) AbeamAnti-human PD-L1 antibody (28-8) Alexa Fluor 647 Abeam Anti-mouse PD-L1antibody Phycoerythrin (10F.9G2) BD Biosciences Rat anti-mouse CD274Antibody PE, APC, BV711 BD Biosciences Mouse anti-human CD274 APC,BB515, BV421, Antibody BV650, BV786, FITC, PE, PE-CF594, PE-Cy7 CellSignaling Anti-human PD-L1 (E1L3N) XP Alexa Fluor 488, Alexa FluorTechnology Rabbit mAb 647, PE

In some instances, an unconjugated anti-PD-L1 antibody may find use inthe herein described methods, including but not limited to e.g., thoseunconjugated anti-PD-L1 antibodies available from commercial suppliersincluding e.g., those commercial suppliers listed above in Table 1. Insome instances, an unconjugated anti-PD-L1 antibody may be conjugatedprior to use including but not limited to e.g., where the unconjugatedantibody is conjugated to a fluorophore.

Anti-PD-L1 protein specific binding members are not limited toantibodies and may also, in some instances, include e.g., anti-PD-L1aptamers, anti-PD-L1 haptens, etc. Additionally, synthetic specificbinding members specific for PD-L1 protein may also be derived from thePD-L1 binding portion of PD-1. For example, in some instances, a PD-L1specific binding member may be rationally designed to include aPD-1-derived PD-L1 binding domain e.g., based on the binding interactionof PD-1 and PD-L1, e.g., as shown in RCSB Protein Data Bank (PDB)structure 4ZQK and described in Zak et al., (2015) Structure23:2341-2348; the disclosure of which is incorporated herein byreference in its entirety.

In some instances, the methods described herein may make use of alabeled binding member specific for PD-L1 transcript. A labeled bindingmember specific for PD-L1 transcript may specifically bind PD-L1 mRNAexpressed in a cell. Useful specific binding members specific for PD-L1transcript include but are not limited to oligonucleotides havingcomplementary sequence to all or a portion of the PD-L1 mRNA sequence.In some instances, a useful oligonucleotide probe may include a sequencecomplementary to a human PD-L1 mRNA transcript including but not limitedto e.g.:

Homo sapiens CD274 molecule (CD274), transcript variant 1, mRNA(NM_014143.3):

(SEQ ID NO: 3) GGCGCAACGCTGAGCAGCTGGCGCGTCCCGCGCGGCCCCAGTTCTGCGCAGCTTCCCGAGGCTCCGCACCAGCCGCGCTTCTGTCCGCCTGCAGGGCATTCCAGAAAGATGAGGATATTTGCTGTCTTTATATTCATGACCTACTGGCATTTGCTGAACGCATTTACTGTCACGGTTCCCAAGGACCTATATGTGGTAGAGTATGGTAGCAATATGACAATTGAATGCAAATTCCCAGTAGAAAAACAATTAGACCTGGCTGCACTAATTGTCTATTGGGAAATGGAGGATAAGAACATTATTCAATTTGTGCATGGAGAGGAAGACCTGAAGGTTCAGCATAGTAGCTACAGACAGAGGGCCCGGCTGTTGAAGGACCAGCTCTCCCTGGGAAATGCTGCACTTCAGATCACAGATGTGAAATTGCAGGATGCAGGGGTGTACCGCTGCATGATCAGCTATGGTGGTGCCGACTACAAGCGAATTACTGTGAAAGTCAATGCCCCATACAACAAAATCAACCAAAGAATTTTGGTTGTGGATCCAGTCACCTCTGAACATGAACTGACATGTCAGGCTGAGGGCTACCCCAAGGCCGAAGTCATCTGGACAAGCAGTGACCATCAAGTCCTGAGTGGTAAGACCACCACCACCAATTCCAAGAGAGAGGAGAAGCTTTTCAATGTGACCAGCACACTGAGAATCAACACAACAACTAATGAGATTTTCTACTGCACTTTTAGGAGATTAGATCCTGAGGAAAACCATACAGCTGAATTGGTCATCCCAGAACTACCTCTGGCACATCCTCCAAATGAAAGGACTCACTTGGTAATTCTGGGAGCCATCTTATTATGCCTTGGTGTAGCACTGACATTCATCTTCCGTTTAAGAAAAGGGAGAATGATGGATGTGAAAAAATGTGGCATCCAAGATACAAACTCAAAGAAGCAAAGTGATACACATTTGGAGGAGACGTAATCCAGCATTGGAACTTCTGATCTTCAAGCAGGGATTCTCAACCTGTGGTTTAGGGGTTCATCGGGGCTGAGCGTGACAAGAGGAAGGAATGGGCCCGTGGGATGCAGGCAATGTGGGACTTAAAAGGCCCAAGCACTGAAAATGGAACCTGGCGAAAGCAGAGGAGGAGAATGAAGAAAGATGGAGTCAAACAGGGAGCCTGGAGGGAGACCTTGATACTTTCAAATGCCTGAGGGGCTCATCGACGCCTGTGACAGGGAGAAAGGATACTTCTGAACAAGGAGCCTCCAAGCAAATCATCCATTGCTCATCCTAGGAAGACGGGTTGAGAATCCCTAATTTGAGGGTCAGTTCCTGCAGAAGTGCCCTTTGCCTCCACTCAATGCCTCAATTTGTTTTCTGCATGACTGAGAGTCTCAGTGTTGGAACGGGACAGTATTTATGTATGAGTTTTTCCTATTTATTTTGAGTCTGTGAGGTCTTCTTGTCATGTGAGTGTGGTTGTGAATGATTTCTTTTGAAGATATATTGTAGTAGATGTTACAATTTTGTCGCCAAACTAAACTTGCTGCTTAATGATTTGCTCACATCTAGTAAAACATGGAGTATTTGTAAGGTGCTTGGTCTCCTCTATAACTACAAGTATACATTGGAAGCATAAAGATCAAACCGTTGGTTGCATAGGATGTCACCTTTATTTAACCCATTAATACTCTGGTTGACCTAATCTTATTCTCAGACCTCAAGTGTCTGTGCAGTATCTGTTCCATTTAAATATCAGCTTTACAATTATGTGGTAGCCTACACACATAATCTCATTTCATCGCTGTAACCACCCTGTTGTGATAACCACTATTATTTTACCCATCGTACAGCTGAGGAAGCAAACAGATTAAGTAACTTGCCCAAACCAGTAAATAGCAGACCTCAGACTGCCACCCACTGTCCTTTTATAATACAATTTACAGCTATATTTTACTTTAAGCAATTCTTTTATTCAAAAACCATTTATTAAGTGCCCTTGCAATATCAATCGCTGTGCCAGGCATTGAATCTACAGATGTGAGCAAGACAAAGTACCTGTCCTCAAGGAGCTCATAGTATAATGAGGAGATTAACAAGAAAATGTATTATTACAATTTAGTCCAGTGTCATAGCATAAGGATGATGCGAGGGGAAAACCCGAGCAGTGTTGCCAAGAGGAGGAAATAGGCCAATGTGGTCTGGGACGGTTGGATATACTTAAACATCTTAATAATCAGAGTAATTTTCATTTACAAAGAGAGGTCGGTACTTAAAATAACCCTGAAAAATAACACTGGAATTCCTTTTCTAGCATTATATTTATTCCTGATTTGCCTTTGCCATATAATCTAATGCTTGTTTATATAGTGTCTGGTATTGTTTAACAGTTCTGTCTTTTCTATTTAAATGCCACTAAATTTTAAATTCATACCTTTCCATGATTCAAAATTCAAAAGATCCCATGGGAGATGGTTGGAAAATCTCCACTTCATCCTCCAAGCCATTCAAGTTTCCTTTCCAGAAGCAACTGCTACTGCCTTTCATTCATATGTTCTTCTAAAGATAGTCTACATTTGGAAATGTATGTTAAAAGCACGTATTTTTAAAATTTTTTTCCTAAATAGTAACACATTGTATGTCTGCTGTGTACTTTGCTATTTTTATTTATTTTAGTGTTTCTTATATAGCAGATGGAATGAATTTGAAGTTCCCAGGGCTGAGGATCCATGCCTTCTTTGTTTCTAAGTTATCTTTCCCATAGCTTTTCATTATCTTTCATATGATCCAGTATATGTTAAATATGTCCTACATATACATTTAGACAACCACCATTTGTTAAGTATTTGCTCTAGGACAGAGTTTGGATTTGTTTATGTTTGCTCAAAAGGAGACCCATGGGCTCTCCAGGGTGCACTGAGTCAATCTAGTCCTAAAAAGCAATCTTATTATTAACTCTGTATGACAGAATCATGTCTGGAACTTTTGTTTTCTGCTTTCTGTCAAGTATAAACTTCACTTTGATGCTGTACTTGCAAAATCACATTTTCTTTCTGGAAATTCCGGCAGTGTACCTTGACTGCTAGCTACCCTGTGCCAGAAAAGCCTCATTCGTTGTGCTTGAACCCTTGAATGCCACCAGCTGTCATCACTACACAGCCCTCCTAAGAGGCTTCCTGGAGGTTTCGAGATTCAGATGCCCTGGGAGATCCCAGAGTTTCCTTTCCCTCTTGGCCATATTCTGGTGTCAATGACAAGGAGTACCTTGGCTTTGCCACATGTCAAGGCTGAAGAAACAGTGTCTCCAACAGAGCTCCTTGTGTTATCTGTTTGTACATGTGCATTTGTACAGTAATTGGTGTGACAGTGTTCTTTGTGTGAATTACAGGCAAGAATTGTGGCTGAGCAAGGCACATAGTCTACTCAGTCTATTCCTAAGTCCTAACTCCTCCTTGTGGTGTTGGATTTGTAAGGCACTTTATCCCTTTTGTCTCATGTTTCATCGTAAATGGCATAGGCAGAGATGATACCTAATTCTGCATTTGATTGTCACTTTTTGTACCTGCATTAATTTAATAAAATATTCTTATTTATTTTGTTACTTGGTACACCAGCATGTCCATTTTCTTGTTTATTTTGTGTTTAATAAAATGTTCAGTTTAACATCCCAGTGGAGAAAGTTAAAAAA orHomo sapiens CD274 molecule (CD274), transcriptvariant 2, mRNA (NM_001267706.1): (SEQ ID NO: 4)GGCGCAACGCTGAGCAGCTGGCGCGTCCCGCGCGGCCCCAGTTCTGCGCAGCTTCCCGAGGCTCCGCACCAGCCGCGCTTCTGTCCGCCTGCAGGGCATTCCAGAAAGATGAGGATATTTGCTGTCTTTATATTCATGACCTACTGGCATTTGCTGAACGCCCCATACAACAAAATCAACCAAAGAATTTTGGTTGTGGATCCAGTCACCTCTGAACATGAACTGACATGTCAGGCTGAGGGCTACCCCAAGGCCGAAGTCATCTGGACAAGCAGTGACCATCAAGTCCTGAGTGGTAAGACCACCACCACCAATTCCAAGAGAGAGGAGAAGCTTTTCAATGTGACCAGCACACTGAGAATCAACACAACAACTAATGAGATTTTCTACTGCACTTTTAGGAGATTAGATCCTGAGGAAAACCATACAGCTGAATTGGTCATCCCAGAACTACCTCTGGCACATCCTCCAAATGAAAGGACTCACTTGGTAATTCTGGGAGCCATCTTATTATGCCTTGGTGTAGCACTGACATTCATCTTCCGTTTAAGAAAAGGGAGAATGATGGATGTGAAAAAATGTGGCATCCAAGATACAAACTCAAAGAAGCAAAGTGATACACATTTGGAGGAGACGTAATCCAGCATTGGAACTTCTGATCTTCAAGCAGGGATTCTCAACCTGTGGTTTAGGGGTTCATCGGGGCTGAGCGTGACAAGAGGAAGGAATGGGCCCGTGGGATGCAGGCAATGTGGGACTTAAAAGGCCCAAGCACTGAAAATGGAACCTGGCGAAAGCAGAGGAGGAGAATGAAGAAAGATGGAGTCAAACAGGGAGCCTGGAGGGAGACCTTGATACTTTCAAATGCCTGAGGGGCTCATCGACGCCTGTGACAGGGAGAAAGGATACTTCTGAACAAGGAGCCTCCAAGCAAATCATCCATTGCTCATCCTAGGAAGACGGGTTGAGAATCCCTAATTTGAGGGTCAGTTCCTGCAGAAGTGCCCTTTGCCTCCACTCAATGCCTCAATTTGTTTTCTGCATGACTGAGAGTCTCAGTGTTGGAACGGGACAGTATTTATGTATGAGTTTTTCCTATTTATTTTGAGTCTGTGAGGTCTTCTTGTCATGTGAGTGTGGTTGTGAATGATTTCTTTTGAAGATATATTGTAGTAGATGTTACAATTTTGTCGCCAAACTAAACTTGCTGCTTAATGATTTGCTCACATCTAGTAAAACATGGAGTATTTGTAAGGTGCTTGGTCTCCTCTATAACTACAAGTATACATTGGAAGCATAAAGATCAAACCGTTGGTTGCATAGGATGTCACCTTTATTTAACCCATTAATACTCTGGTTGACCTAATCTTATTCTCAGACCTCAAGTGTCTGTGCAGTATCTGTTCCATTTAAATATCAGCTTTACAATTATGTGGTAGCCTACACACATAATCTCATTTCATCGCTGTAACCACCCTGTTGTGATAACCACTATTATTTTACCCATCGTACAGCTGAGGAAGCAAACAGATTAAGTAACTTGCCCAAACCAGTAAATAGCAGACCTCAGACTGCCACCCACTGTCCTTTTATAATACAATTTACAGCTATATTTTACTTTAAGCAATTCTTTTATTCAAAAACCATTTATTAAGTGCCCTTGCAATATCAATCGCTGTGCCAGGCATTGAATCTACAGATGTGAGCAAGACAAAGTACCTGTCCTCAAGGAGCTCATAGTATAATGAGGAGATTAACAAGAAAATGTATTATTACAATTTAGTCCAGTGTCATAGCATAAGGATGATGCGAGGGGAAAACCCGAGCAGTGTTGCCAAGAGGAGGAAATAGGCCAATGTGGTCTGGGACGGTTGGATATACTTAAACATCTTAATAATCAGAGTAATTTTCATTTACAAAGAGAGGTCGGTACTTAAAATAACCCTGAAAAATAACACTGGAATTCCTTTTCTAGCATTATATTTATTCCTGATTTGCCTTTGCCATATAATCTAATGCTTGTTTATATAGTGTCTGGTATTGTTTAACAGTTCTGTCTTTTCTATTTAAATGCCACTAAATTTTAAATTCATACCTTTCCATGATTCAAAATTCAAAAGATCCCATGGGAGATGGTTGGAAAATCTCCACTTCATCCTCCAAGCCATTCAAGTTTCCTTTCCAGAAGCAACTGCTACTGCCTTTCATTCATATGTTCTTCTAAAGATAGTCTACATTTGGAAATGTATGTTAAAAGCACGTATTTTTAAAATTTTTTTCCTAAATAGTAACACATTGTATGTCTGCTGTGTACTTTGCTATTTTTATTTATTTTAGTGTTTCTTATATAGCAGATGGAATGAATTTGAAGTTCCCAGGGCTGAGGATCCATGCCTTCTTTGTTTCTAAGTTATCTTTCCCATAGCTTTTCATTATCTTTCATATGATCCAGTATATGTTAAATATGTCCTACATATACATTTAGACAACCACCATTTGTTAAGTATTTGCTCTAGGACAGAGTTTGGATTTGTTTATGTTTGCTCAAAAGGAGACCCATGGGCTCTCCAGGGTGCACTGAGTCAATCTAGTCCTAAAAAGCAATCTTATTATTAACTCTGTATGACAGAATCATGTCTGGAACTTTTGTTTTCTGCTTTCTGTCAAGTATAAACTTCACTTTGATGCTGTACTTGCAAAATCACATTTTCTTTCTGGAAATTCCGGCAGTGTACCTTGACTGCTAGCTACCCTGTGCCAGAAAAGCCTCATTCGTTGTGCTTGAACCCTTGAATGCCACCAGCTGTCATCACTACACAGCCCTCCTAAGAGGCTTCCTGGAGGTTTCGAGATTCAGATGCCCTGGGAGATCCCAGAGTTTCCTTTCCCTCTTGGCCATATTCTGGTGTCAATGACAAGGAGTACCTTGGCTTTGCCACATGTCAAGGCTGAAGAAACAGTGTCTCCAACAGAGCTCCTTGTGTTATCTGTTTGTACATGTGCATTTGTACAGTAATTGGTGTGACAGTGTTCTTTGTGTGAATTACAGGCAAGAATTGTGGCTGAGCAAGGCACATAGTCTACTCAGTCTATTCCTAAGTCCTAACTCCTCCTTGTGGTGTTGGATTTGTAAGGCACTTTATCCCTTTTGTCTCATGTTTCATCGTAAATGGCATAGGCAGAGATGATACCTAATTCTGCATTTGATTGTCACTTTTTGTACCTGCATTAATTTAATAAAATATTCTTATTTATTTTGTTACTTGGTACACCAGCATGTCCATTTTCTTGTTTATTTTGTGTTTAATAAAATGTTCAGTTTAACATCCCAGTGGAGAAAGTTAAAAAA.

Useful oligonucleotide probes may be DNA or RNA based and may includebut are not limited to those probes used in in situ hybridization,including e.g., DNA in situ hybridization probes, RNA in situhybridization probes (e.g., riboprobes), as well as anti-sense probeshaving one or more synthetic components including e.g., one or moresynthetic nucleoside bases (such as e.g., a locked nucleic acid (LNA)and the like). Such probes may vary in length, ranging in some instancesfrom 13 to 100 nt, such as 14 to 50 nt, e.g., 15 to 25 nt, etc.Oligonucleotide probes may be directly conjugated with a fluorophore,including e.g., those fluorophores described herein. In some instances,oligonucleotide probes may be conjugated with a moiety that allows forbinding of a label once the oligonucleotide is hybridized. For example,an oligonucleotide may be conjugated to one or more biotin moleculesallowing the oligonucleotide to be labeled after hybridization e.g., byintroducing fluorescently labeled streptavidin.

Reagents useful in the herein described methods may also include labeledspecific binding members specific for immune cells. Such specificbinding members may allow for the identification of immune cells withina cell population of the instant disclosure and/or identification of acell as not being an immune cell as described above.

Any convenient labeled specific binding member for an immune cell mayfind use in the herein described methods including but not limited toe.g., antibodies specific for individual immune cell markers includingbut not limited to e.g., an anti-CD114 antibody, an anti-CD117 antibody,an anti-CD11a antibody, an anti-CD11b antibody, an anti-CD14 antibody,an anti-CD15 antibody, an anti-CD16 antibody, an anti-CD182 antibody, ananti-CD19 antibody, an anti-CD20 antibody, an anti-CD22 antibody, ananti-CD24 antibody, an anti-CD25 antibody, an anti-CD3 antibody, ananti-CD30 antibody, an anti-CD31 antibody, an anti-CD34 antibody, ananti-CD38 antibody, an anti-CD4 antibody, an anti-CD45 antibody, ananti-CD56 antibody, an anti-CD61 antibody, an anti-CD8 antibody, ananti-CD91 antibody, an anti-Foxp3 antibody, and the like. Accordingly,in some instances, a detected neoplasia cell may be furthercharacterized as lacking expression of or having expression of below apredetermined threshold of one or more immune cell markers, e.g., asdetected using an antibody to an immune cell marker including e.g.,those listed above.

As described above, e.g., regarding the detection of DNA content, theherein described methods may include detection of DNA using one or moreDNA labeling reagents. Various DNA labeling reagents may find use in theherein described methods including but not limited to: Hoechst 33342(2′-(4-Ethoxyphenyl)-5-(4-methyl-1-piperazinyl)-1H,1′H-2,5′-bibenzimidazoletrihydrochloride) and Hoechst 33258(4-[6-(4-Methyl-1-piperazinyl)-1′,3′-dihydro-1H,2′H-2,5′-bibenzimidazol-2′-ylidene]-2,5-cyclohexadien-1-onetrihydrochloride) and others of the Hoechst series; SYTO 40, SYTO 11,12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25 (green); SYTO 17, 59 (red),DAPI, DRAQ5™ (an anthraquinone dye with high affinity for doublestranded DNA), YOYO-1, propidium iodide, YO-PRO-3, TO-PRO-3, YOYO-3 andTOTO-3, SYTOX Green, SYTOX, methyl green, acridine homodimer,7-aminoactinomycin D, 9-amino-6-chloro-2-methoxyactridine.

The above-described markers include intracellular markers. As usedherein, the term “intracellular markers” refers to components of thecell that are within the cell beyond the outer surface of the plasmamembrane. Such components may be or may be within any interior componentof the cell including but not limited to the inner surface of the plasmamembrane, the cytoplasm, the nucleus, mitochondria, endoplasmicreticulum, etc. As such, labeling or detection of intracellular markersrequires transport of a specific label or specific binding agent of theintracellular marker across at least the outer surface of the plasmamembrane. In some instances, a label or specific binding agent for anintracellular marker may be membrane permeable thus not requiringmodulation of membrane permeability for labeling of the intracellularmarker. In some embodiments, a label or specific binding agent for anintracellular marker may be membrane impermeable thus requiringmodulation of membrane permeability for labeling of the intracellularmarker, including, e.g., preparation and or treatment of the cells withone or more permeabilizing reagents as described herein.

The above-described markers include cell surface markers. As usedherein, the term “cell surface markers” refers to components of the cellthat are at least exposed, partially or completely, on the outer surfaceof the plasma membrane of cell and thus may be accessed withoutmodulating cell permeability, e.g., without the use of one or morepermeabilizing reagents as described herein. In some instances, cellsurface markers include components of the cell that have a portionexposed on the outer surface of the cell membrane but also contain anintracellular portion and/or a transmembrane portion.

As described herein and as will be readily apparent to one or ordinaryskill in the art, any combination of the agents and labels describedherein may be employed in the methods described provided the combinationis appropriate and the components do not physically or opticallyinterfere. For example, where alterations or substitutions of particularlabels can and/or should be employed in order to allow for thecombination of two or more desired components is within the skill of theordinary artisan. As a non-limiting example, where a particularfluorescent label of a biomarker interferes optically (e.g., has anoverlapping emission spectra) with a desired DNA labeling agent of aparticular emission wavelength, the fluorescent label of the biomarkermay be substituted with a different fluorescent label having no or lessemission spectra overlap with the desired DNA labeling agent.

Methods of Treating

As summarized above, the present disclosure includes methods of treatinga subject for a neoplasia. The terms “subject,” “individual,” “host,”and “patient,” are used interchangeably herein and refer to anymammalian subject for whom diagnosis, treatment, or therapy is desired,particularly humans.

Aspects of the subject methods generally include identifying ananti-PD-1/PD-L1 immunotherapy responsive neoplasia in a subject andtreating the subject by administering to the subject an anti-PD-1/PD-L1immunotherapy. Identifying a neoplasia in a subject as ananti-PD-1/PD-L1 immunotherapy responsive may be performed according toany of the methods described herein and will generally includecytometrically detecting a cell of the neoplasia that expresses PD-L1above a predetermined threshold.

Subjects treated according to the herein described methods includesubjects having a neoplasia suspected of expressing PD-L1. In someinstances, subjects treated according to the herein described methodsmay be subjects having a neoplasia suspected of or showing symptoms ofimmune evasion. Various indicators may suggest immune evasion by aneoplasia including but not limited to e.g., tumor growth orprogression, immunosuppression, unresponsiveness to immunotherapy, andthe like. Various factors and events present in the tumormicroenvironment may be directly indicative of immune evasion or tumorprogression, which indirectly indicates immune evasion, including butnot limited to e.g., presence of activated T cells in the absence ofappropriate costimulation, tumor cell expression of T cell-inhibitorymolecules (e.g., HLA-G, HLA-E, etc.), tumor antigen loss, downregulationof MHC molecules, regulatory T cells (Tregs) (e.g., CD4+ CD25+ Tregs,CD4+ CD25+ FoxP3+, etc.), presence of CD1d-restricted T cells,immunosuppressive factors and tumor-derived cytokines (e.g.,transforming growth factor (TGF)-β, tumor necrosis factor (TNF)-α, VEGF,IL-1, IL-1 β, IL-6, IL-8, IL-10, GM-CSF, type I IFNs, gangliosides,receptor-binding cancer-associated surface antigen (RCAS1), etc.),presence of immunosuppressive myeloid cell populations (immature myeloidcell populations e.g., those expressing iNOS (also known as NOS2) orarginase 1 (ARG1), myeloid-derived suppressor cells (MDSCs), modulateddendritic cells (DCs), alternatively-activated M1 and M2 macrophages,CD11b+ Gr1+ MDSCs, etc.), TCR ζ-chain downregulation, upregulation ofimmunosuppressive enzymes (e.g., indoleamine 2,3-dioxygenase (IDO),arginase, inhibitor of nuclear factor kappa-B kinase (IKK)2, etc.), andthe like. In some instances, particular tumor characteristics may alsobe indicative of immune evasion, including but not limited to e.g.,tumor resistance to cytotoxic pathways (e.g., as seen in tumors with FASmutations), mutations in the gene encoding the TRAIL receptor deathreceptor 5 (DR5), overexpression of the anti-apoptotic molecules (e.g.,FLIP, BCL-XL, etc.), and the like.

In some instances, the herein described methods of detectinganti-PD-1/PD-L1 immunotherapy responsive cells in a subject may serve tolimit the administration of an anti-PD-1/PD-L1 immunotherapy to asubject having an immune-related disorder or a subject that is atincreased risk of developing an immune-related disorder. By virtue ofbeing naturally expressed on immune cells, PD-L1 targeted therapies cannegatively impact immune cells of a subject. In some instances, themethods of the present disclosure may be used to screen subjects priorto anti-PD-1/PD-L1 immunotherapy, including e.g., those subjects mostlikely to be negatively impacted by anti-PD-1/PD-L1 immunotherapy orhave adverse events due to anti-PD-1/PD-L1 immunotherapy, includinge.g., those subjects with immune-related disorders.

Non-limiting examples of immune-related disorders include but are notlimited to e.g., autoimmune disorders such as e.g., Acute DisseminatedEncephalomyelitis (ADEM), Acute necrotizing hemorrhagicleukoencephalitis, Addison's disease, Agammaglobulinemia, Alopeciaareata, Amyloidosis, Ankylosing spondylitis, Anti-GBM/Anti-TBMnephritis, Antiphospholipid syndrome (APS), Autoimmune angioedema,Autoimmune aplastic anemia, Autoimmune dysautonomia, Autoimmunehepatitis, Autoimmune hyperlipidemia, Autoimmune immunodeficiency,Autoimmune inner ear disease (AIED), Autoimmune myocarditis, Autoimmuneoophoritis, Autoimmune pancreatitis, Autoimmune retinopathy, Autoimmunethrombocytopenic purpura (ATP), Autoimmune thyroid disease, Autoimmuneurticaria, Axonal & neuronal neuropathies, Balo disease, Behcet'sdisease, Bullous pemphigoid, Cardiomyopathy, Castleman disease, Celiacdisease, Chagas disease, Chronic fatigue syndrome, Chronic inflammatorydemyelinating polyneuropathy (CIDP), Chronic recurrent multifocalostomyelitis (CRMO), Churg-Strauss syndrome, Cicatricialpemphigoid/benign mucosal pemphigoid, Crohn's disease, Cogans syndrome,Cold agglutinin disease, Congenital heart block, Coxsackie myocarditis,CREST disease, Essential mixed cryoglobulinemia, Demyelinatingneuropathies, Dermatitis herpetiformis, Dermatomyositis, Devic's disease(neuromyelitis optica), Discoid lupus, Dressler's syndrome,Endometriosis, Eosinophilic esophagitis, Eosinophilic fasciitis,Erythema nodosum, Experimental allergic encephalomyelitis, Evanssyndrome, Fibromyalgia, Fibrosing alveolitis, Giant cell arteritis(temporal arteritis), Giant cell myocarditis, Glomerulonephritis,Goodpasture's syndrome, Granulomatosis with Polyangiitis (GPA) (formerlycalled Wegener's Granulomatosis), Graves' disease, Guillain-Barresyndrome, Hashimoto's encephalitis, Hashimoto's thyroiditis, Hemolyticanemia, Henoch-Schonlein purpura, Herpes gestationis,Hypogammaglobulinemia, Idiopathic thrombocytopenic purpura (ITP), IgAnephropathy, IgG4-related sclerosing disease, Immunoregulatorylipoproteins, Inclusion body myositis, Interstitial cystitis, Juvenilearthritis, Juvenile diabetes (Type 1 diabetes), Juvenile myositis,Kawasaki syndrome, Lambert-Eaton syndrome, Leukocytoclastic vasculitis,Lichen planus, Lichen sclerosus, Ligneous conjunctivitis, Linear IgAdisease (LAD), Lupus (SLE), Lyme disease, chronic, Meniere's disease,Microscopic polyangiitis, Mixed connective tissue disease (MCTD),Mooren's ulcer, Mucha-Habermann disease, Multiple sclerosis, Myastheniagravis, Myositis, Narcolepsy, Neuromyelitis optica (Devic's),Neutropenia, Ocular cicatricial pemphigoid, Optic neuritis, Palindromicrheumatism, PANDAS (Pediatric Autoimmune Neuropsychiatric DisordersAssociated with Streptococcus), Paraneoplastic cerebellar degeneration,Paroxysmal nocturnal hemoglobinuria (PNH), Parry Romberg syndrome,Parsonnage-Turner syndrome, Pars planitis (peripheral uveitis),Pemphigus, Peripheral neuropathy, Perivenous encephalomyelitis,Pernicious anemia, POEMS syndrome, Polyarteritis nodosa, Type I, II, &III autoimmune polyglandular syndromes, Polymyalgia rheumatica,Polymyositis, Postmyocardial infarction syndrome, Postpericardiotomysyndrome, Progesterone dermatitis, Primary biliary cirrhosis, Primarysclerosing cholangitis, Psoriasis, Psoriatic arthritis, Idiopathicpulmonary fibrosis, Pyoderma gangrenosum, Pure red cell aplasia,Raynauds phenomenon, Reactive Arthritis, Reflex sympathetic dystrophy,Reiter's syndrome, Relapsing polychondritis, Restless legs syndrome,Retroperitoneal fibrosis, Rheumatic fever, Rheumatoid arthritis,Sarcoidosis, Schmidt syndrome, Scleritis, Scleroderma, Sjogren'ssyndrome, Sperm & testicular autoimmunity, Stiff person syndrome,Subacute bacterial endocarditis (SBE), Susac's syndrome, Sympatheticophthalmia, Takayasu's arteritis, Temporal arteritis/Giant cellarteritis, Thrombocytopenic purpura (TTP), Tolosa-Hunt syndrome,Transverse myelitis, Type 1 diabetes, Ulcerative colitis,Undifferentiated connective tissue disease (UCTD), Uveitis, Vasculitis,Vesiculobullous dermatosis, Vitiligo, Wegener's granulomatosis (nowtermed Granulomatosis with Polyangiitis (GPA), and the like.

In some instances, immune-related disorders may also include anactivated immune system, e.g., as present in a subject fighting aninfection or other immune stimulating condition.

In some instances, a subject with a neoplasia may be tested to determinewhether one or more cells of the subject's neoplasia expresses PD-L1above a predetermined threshold and, if the one or more cells isdetected, the subject may be subsequently treated with ananti-PD-1/PD-L1 immunotherapy. Any neoplasia may be assayed to assessthe likelihood that the subject's neoplasia is anti-PD-1/PD-L1immunotherapy responsiveness, including whether or not the subject'sneoplasia has previously shown indicators of immune evasion.

In some instances, a subject diagnosed with a neoplasia is assessed todetermine the likelihood of responsiveness to anti-PD-1/PD-L1immunotherapy, as described herein, prior to receiving any othertreatment for the neoplasia. In some instances, a subject diagnosed witha neoplasia is assessed to determine the likelihood of responsiveness toanti-PD-1/PD-L1 immunotherapy, as described herein, while receiving acourse of therapy for the neoplasia. In some instances, a subjectdiagnosed with a neoplasia is assessed to determine the likelihood ofresponsiveness to anti-PD-1/PD-L1 immunotherapy, as described herein,after receiving a course of therapy for the neoplasia.

Neoplasia therapies that may be administered to a subject before, duringor after a subject is assessed for anti-PD-1/PD-L1 immunotherapyresponsiveness will vary depending on numerous factors including e.g.,the type of neoplasia, the subject's medical history, general state ofhealth and/or any co-morbidities, and the like. Useful neoplasiatherapies include but are not limited to e.g., radiation therapy,chemotherapy, immunotherapy, and the like. Neoplasia therapies, such asbut not limited to radiation therapy, chemotherapy, immunotherapy, andthe like, may be administered locally or systemically.

In some instances, a subject may be assessed for anti-PD-1/PD-L1immunotherapy responsiveness before a course of therapy is begunincluding but not limited to e.g., immunotherapy. For example, in someinstances, a medical professional may assay a subject to determine theanti-PD-1/PD-L1 immunotherapy responsiveness of the subject's cancerprior to administering an anti-PD-1/PD-L1 immunotherapy and the medicalprofessional may administer the therapy only if the subject's neoplasiais identified as likely to be anti-PD-1/PD-L1 immunotherapy responsive,e.g., through the detection of one or more cells expressing PD-L1 abovea predetermined threshold.

The amount of time before starting a course of treatment that a subjectmay be assessed to determine whether the neoplasia of the subject isanti-PD-1/PD-L1 immunotherapy responsive may vary and may range from 1day or less to a month or more including but not limited to e.g., 1 day,2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 1month, etc. In some instances, a course of treatment may be begun thesame day that an assessment for anti-PD-1/PD-L1 immunotherapyresponsiveness of a subject's neoplasia is performed.

In some instances, a subject may be assessed for anti-PD-1/PD-L1immunotherapy responsiveness after a course of treatment has alreadybeen administered. For example, in some instances, a subject's neoplasiamay be assayed for anti-PD-1/PD-L1 immunotherapy responsiveness after afailed course of immunotherapy, including but not limited to e.g.,anti-PD-1/PD-L1 immunotherapy. In some instances, if the assessmentidentifies the neoplasia as anti-PD-1/PD-L1 immunotherapy responsivethen the anti-PD-1/PD-L1 immunotherapy may be attempted a second time.In some instances, if the assessment identifies the neoplasia as notanti-PD-1/PD-L1 immunotherapy responsive, then the medical professionalmay not attempt anti-PD-1/PD-L1 immunotherapy a second time. In someinstances, an assessment indicating that a neoplasia is notanti-PD-1/PD-L1 immunotherapy responsive may indicate that anothercourse of therapy (e.g., non-PD-L1 immunotherapy, chemotherapy,radiation therapy, etc.) is warranted.

The amount of time after a course of treatment has ended that a subjectmay be assessed to determine whether the neoplasia of the subject isanti-PD-1/PD-L1 immunotherapy responsive may vary and may range from 1day or less to a month or more including but not limited to e.g., 1 day,2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 1month, etc. In some instances, an assessment for anti-PD-1/PD-L1immunotherapy responsiveness of a subject's neoplasia is performed thesame day on which the course of therapy is ended. In some instances, anassessment for anti-PD-1/PD-L1 immunotherapy responsiveness may beperformed during a long-term follow-up assessment of a subject. Thelength of time after a course of treatment at which point long-termfollow-up is performed will vary and may range from 3 months or less to10 years or more including but not limited to e.g., 3 months, 4 months,5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months,one year, 1.5 years, 2 years, 3 years, 4 years, 5 years, 6 years, 7years, 8 years, 9 years, 10 years, etc.

In some instances, an assessment of whether a subject has ananti-PD-1/PD-L1 immunotherapy responsive neoplasia may be performedduring a course of therapy to treat the subject for the neoplasia. Forexample, a course of therapy to treat a subject for a neoplasia may bebegun and during the course of therapy one or more assessments ofanti-PD-1/PD-L1 immunotherapy responsiveness may be performed, e.g., tomonitor the therapy. In some instances, a subject may be receiving acourse of immunotherapy, including e.g., a course of anti-PD-1/PD-L1immunotherapy, and one or more assessments of the anti-PD-1/PD-L1immunotherapy responsiveness of the subject's neoplasia may be performedduring the immunotherapy. Such assessments may be performed for avariety of reasons including but not limited to e.g., the assess whetherto continue the immunotherapy, to assess whether to alter the course ofimmunotherapy (e.g., change the immunotherapy drug being administered,change the dose of immunotherapy drug being administered, change thefrequency of administration, etc.). For example, if an assessment duringa course of therapy indicates that the subject's neoplasia isanti-PD-1/PD-L1 immunotherapy responsive then the subject may beswitched to an anti-PD-1/PD-L1 immunotherapy or the subject's dose of ananti-PD-1/PD-L1 immunotherapy may be increased or the frequency ofadministering the subject an anti-PD-1/PD-L1 immunotherapy may beincreased. Conversely, if an assessment during a course of therapyindicates that the subject's neoplasia is not anti-PD-1/PD-L1immunotherapy responsive then the subject may be switched to anon-anti-PD-1/PD-L1 immunotherapy or the subject's dose of ananti-PD-1/PD-L1 immunotherapy may be decreased or terminated or thefrequency of administering the subject an anti-PD-1/PD-L1 immunotherapymay be decreased or terminated.

Assessments made during a course of treatment may also be referred toherein as monitoring, including monitoring anti-PD-1/PD-L1 immunotherapyresponsiveness. Besides monitoring subjects receiving anti-PD-1/PD-L1immunotherapy for anti-PD-1/PD-L1 immunotherapy responsiveness, thesubject methods also include monitoring a neoplasia of a subject foranti-PD-1/PD-L1 immunotherapy responsiveness during the course of atreatment that is not an anti-PD-1/PD-L1 immunotherapy treatment. Forexample, in some instances, a subject undergoing radiation therapy maybe monitored for anti-PD-1/PD-L1 immunotherapy responsiveness and, ifthe subject's neoplasia is identified as anti-PD-1/PD-L1 immunotherapyresponsive then a course of anti-PD-1/PD-L1 immunotherapy may beinitiated, in conjunction with or instead of the radiation therapy. Insome instances, a subject undergoing chemotherapy may be monitored foranti-PD-1/PD-L1 immunotherapy responsiveness and, if the subject'sneoplasia is identified as anti-PD-1/PD-L1 immunotherapy responsive thena course of anti-PD-1/PD-L1 immunotherapy may be initiated, inconjunction with or instead of the chemotherapy. In some instances, asubject undergoing non-anti-PD-1/PD-L1 immunotherapy (i.e.,immunotherapy having a target other than PD-L1 or PD-1) may be monitoredfor anti-PD-1/PD-L1 immunotherapy responsiveness and, if the subject'sneoplasia is identified as anti-PD-1/PD-L1 immunotherapy responsive thena course of anti-PD-1/PD-L1 immunotherapy may be initiated, inconjunction with or instead of the non-anti-PD-1/PD-L1 immunotherapy.

Methods of treating a subject having a neoplasia that is or is predictedto be anti-PD-1/PD-L1 immunotherapy responsive will generally includeadministering the subject an anti-PD-1/PD-L1 immunotherapy. Anyanti-PD-1/PD-L1 immunotherapy may find use in the subject methodsincluding but not limited to e.g., those therapies that includeadministering to a subject an effective amount of one or moreanti-PD-1/PD-L1 therapeutic antagonists where such antagonists includebut are not limited to e.g., OPDIVO® (nivolumab), KEYTRUDA®(pembrolizumab), Tecentriq™ (atezolizumab), durvalumab (MEDI4736),avelumab (MSB0010718C), BMS-936559 (MDX-1105), CA-170, BMS-202, BMS-8,BMS-37, BMS-242 and the like.

Nivolumab (OPDIVO®) is a humanized IgG4 anti-PD-1 monoclonal antibodyused to treat cancer. Pembrolizumab (KEYTRUDA®), formerly known asMK-3475, lambrolizumab, etc., is a humanized antibody used in cancerimmunotherapy targeting the PD-1 receptor. Atezolizumab (Tecentriq™) isa fully humanized, engineered monoclonal antibody of IgG1 isotypeagainst the PD-L1 protein. Durvalumab (MedImmune) is a therapeuticmonoclonal antibody that targets PD-L1. Avelumab (also known asMSB0010718C; Merck KGaA, Darmstadt, Germany & Pfizer) is a fully humanmonoclonal PD-L1 antibody of isotype IgG1. BMS-936559 (also known asMDX-1105; Bristol-Myers Squibb) is a blocking antibody that has beenshown to bind to PD-L1 and prevent its binding to PD-1 (see e.g., U.S.NIH Clinical Trial No. NCT00729664). CA-170 (Curis, Inc.) is a smallmolecule PD-L1 antagonist. BMS-202, BMS-8, BMS-37, BMS-242 are smallmolecule PD-1/PD-L1 complex antagonists that bind PD-1 (see e.g., Kaz etal., (2016) Oncotarget 7(21); the disclosure of which is incorporatedherein by reference in its entirety).

Anti-PD-L1 antagonists, including e.g., antibodies, useful in themethods described herein include but are not limited to e.g., thosedescribed in U.S. Pat. Nos. 7,722,868; 7,794,710; 7,892,540; 7,943,743;8,168,179; 8,217,149; 8,354,509; 8,383,796; 8,460,927; 8,552,154;8,741,295; 8,747,833; 8,779,108; 8,952,136; 8,981,063; 9,045,545;9,102,725; 9,109,034; 9,175,082; 9,212,224; 9,273,135 and 9,402,888; thedisclosures of which are incorporated herein by reference in theirentirety.

Anti-PD-1 antagonists, including e.g., antibodies, useful in the methodsdescribed herein include but are not limited to e.g., those described in6,808,710; 7,029,674; 7,101,550; 7,488,802; 7,521,051; 8,008,449;8,088,905; 8,168,757; 8,460,886; 8,709,416; 8,951,518; 8,952,136;8,993,731; 9,067,998; 9,084,776; 9,102,725; 9,102,727; 9,102,728;9,109,034; 9,181,342; 9,205,148; 9,217,034; 9,220,776; 9,308,253;9,358,289; 9,387,247 and 9,402,899; the disclosures of which areincorporated herein by reference in their entirety.

Compositions that include one or more of the subject anti-PD-1/PD-L1antagonists may be administered once per day, a few or several times perday, or even multiple times per day, depending upon, among other things,the indication being treated and the judgment of the prescribingphysician.

Methods of administration may be chosen depending on the condition beingtreated and the pharmaceutical composition being administered, such ase.g., the anti-PD-1/PD-L1 pharmaceutical composition being administered.Administration of the subject agent(s) can be done in a variety of ways,including, but not limited to, local administration of the agent,including e.g., subcutaneously, intravenously, intraperitoneally,intramuscularly, and possibly direct injection to specified organs ortumors, although systemic administration may also be used.Administration of the pharmaceutical compositions may be through asingle route or concurrently by several routes.

By “effective amount” is meant an amount sufficient to have atherapeutic effect. A effective amount that will treat a neoplasia willmodulate the symptoms and/or the size of the neoplasia typically by atleast about 1%, including but not limited to e.g., at least about 10%;at least about 20%; at least about 30%; at least about 50%. Such willresult in, e.g., statistically significant and quantifiable changes inthe numbers of cells being affected. This may be a decrease in the sizeof the primary tumor, a decrease in the numbers of micrometastases indistant organs, a decrease in recurrent metastatic disease, etc.

The methods of the present disclosure may, in some embodiments, providefor certain advantages such as but not limited to e.g., improveddetection of a particular cell type, improved treatment decisions and/orimproved treatment outcomes, and the like. Improved detection mayinclude detection with improved specificity, detection with improvedsensitivity, and detection with improved sensitivity and specificity.Advantages of improved detection may also include, in some embodiments,detection that is more efficient, more convenient, and/or morecost-effective. Improved treatment decisions include not only thosedecisions resulting in improved treatment outcomes, but also, in someinstances, improved decisions as to whether or not to treat a subject,decisions preventing needless administration of an agent, treatmentsthat are more cost-effective, efficient, and/or convenient, and thelike. Other advantages, in some embodiments, may include but are notlimited to reducing the number and/or different types of samples thatneed to be collected from a subject and/or analyzed, improved adherencewith a specified treatment regimen, improved patient confidence in aprescribed treatment regimen, and the like.

Kits

Also provided are kits for practicing one or more of the above-describedmethods. The subject kits may vary greatly. Reagents and devicesincluded in the subject kits include those mentioned above with respectto the methods of detecting a neoplastic cell that expresses PD-L1 abovea predetermined threshold.

These would include, for example, specific binding members for PD-L1,including, for example, an antibody specific for PD-L1. Subject kits mayfurther include one or more sample preparation reagents including butnot limited to, e.g., cell fixatives, cell permeabilizing reagents, celllabeling reagents, buffers, diluents, etc. The above components may bepresent in separate containers or one or more components may be combinedinto a single container, e.g., a glass or plastic vial. In someinstances, kits of the instant disclosure may further include a samplepreparation device such as e.g., a homogenizer.

Kits may further include sample obtainment devices, e.g., bloodcollection devices or biopsy collection devices. Non-limiting examplesof biopsy collection devices include but are not limited to e.g., needlebiopsy devices, core biopsy devices, punch biopsy devices, surgicalbiopsy devices, vacuum assisted biopsy devices, etc. In some instances,kits may further include one or more reagents and/or devices for celldissociation including but not limited to e.g., enzymes, enzymeinhibitors, detergents, cell dissociation media or buffer, vortexdevices, nutating devices, rocking devices, etc. Subject kits mayfurther include control reagents and samples including but not limitedto, e.g., control cell samples (e.g., positive control cellular samples,negative control cellular samples, etc.) calibration reagents (e.g.,fluorescent beads, pre-labeled cells, etc.).

In addition to the above components, the subject kits may furtherinclude instructions for practicing the subject methods. Theseinstructions may be present in the subject kits in a variety of forms,one or more of which may be present in the kit. One form in which theseinstructions may be present is as printed information on a suitablemedium or substrate, e.g., a piece or pieces of paper on which theinformation is printed, in the packaging of the kit, in a packageinsert, etc. Yet another means would be a computer readable medium,e.g., diskette, CD, etc., on which the information has been recorded.Yet another means that may be present is a website address which may beused via the internet to access the information at a removed site. Anyconvenient means may be present in the kits.

Notwithstanding the appended claims, the disclosure is also defined bythe following clauses:

1. A method of detecting whether a neoplastic cell that expressesprogrammed-death ligand 1 (PD-L1) above a predetermined threshold ispresent in a neoplasia sample, the method comprising:

-   -   contacting the neoplasia sample with a labeled binding member        specific for PD-L1 to generate a labeled cell suspension;    -   cytometrically assaying the labeled cell suspension to quantify        per cell PD-L1 expression to detect whether a neoplastic cell        that expresses PD-L1 above a predetermined threshold is present        in the neoplasia sample.        2. The method according to Clause 1, wherein the cytometrically        assaying further comprises assaying cell cycle.        3. The method according to Clause 2, wherein assaying cell cycle        comprises quantifying per cell DNA content.        4. The method according to Clause 2 or 3, wherein assaying cell        cycle comprises detecting an expressed cell cycle marker.        5. The method according to any of the preceding clauses, wherein        the method further comprises contacting the cell suspension        sample with a DNA labeling reagent.        6. The method according to any of the preceding clauses, wherein        the method further comprises contacting the neoplasia sample        with a labeled binding member specific for an expressed cell        cycle marker.        7. The method according to any of the preceding clauses, wherein        the cytometrically assaying further comprises assaying        aneuploidy.        8. The method according to any of the preceding clauses, wherein        the detected cell is proliferative.        9. The method according to any of the preceding clauses, wherein        the detected cell is aneuploid.        10. The method according to any of the preceding clauses,        wherein the labeling further comprises contacting the neoplasia        sample with at least one labeled binding member specific for        immune cells.        11. The method according to Clause 10, wherein the at least one        labeled binding member specific for immune cells comprises a        labeled binding member specific for lymphocyte marker CD45.        12. The method according to Clause 10 or 11, wherein the at        least one labeled binding member specific for immune cells        comprises a labeled binding member specific for lymphocyte        marker CD8.        13. The method according to any of Clauses 10-12, wherein the        method comprises detecting cells that are negative for at least        one marker of immune cells.        14. The method according to any of the preceding clauses,        wherein the neoplasia sample is a body fluid sample.        15. The method according to Clause 14, wherein the body fluid        sample is a blood sample.        16. The method according to Clause 14 or 15, wherein the        detected cell is circulating tumor cell.        17. The method according to any of Clauses 14-16, wherein the        detected cell is a hematopoietic cancer cell.        18. The method according to any of Clauses 1 to 13, wherein the        neoplasia sample is a solid tumor sample.        19. The method according to Clause 18, wherein the solid tumor        is an epithelial tumor.        20. The method according to Clause 18 or 19, wherein the solid        tumor is a lung cancer tumor.        21. The method according to Clause 20, wherein the lung cancer        tumor is a non-small cell lung cancer (NSCLC) tumor.        22. The method according to Clause 18 or 19, wherein the solid        tumor is a breast cancer tumor.        23. The method according to any of Clauses 18 to 22, wherein the        detected cells comprise squamous cell carcinoma cells.        24. The method according to any of Clauses 18 to 22, wherein the        detected cells comprise adenocarcinoma cells.        25. The method according to any of Clauses 18 to 22, wherein the        detected cells comprise adenosquamous carcinoma cells.        26. The method according to any of the preceding clauses,        wherein the neoplasia sample is prepared from a biopsy.        27. The method according to Clause 26, wherein the biopsy is a        solid tissue biopsy.        28. The method according to Clause 27, wherein the method        further comprises preparing the neoplasia sample from the solid        tissue biopsy.        29. The method of Clause 28, wherein preparing the neoplasia        sample from the solid tissue biopsy comprises homogenizing        tissue of the solid tissue biopsy.        30. The method according to Clause 26, wherein the biopsy is a        liquid biopsy.        31. The method according to Clause 30, wherein the method        further comprises preparing the neoplasia sample from the liquid        biopsy.        32. The method according to Clause 26, wherein the biopsy is a        fine needle aspiration (FNA) biopsy.        33. The method according to Clause 32, wherein the method        further comprises preparing the neoplasia sample from the FNA        biopsy.        34. The method according to any of the preceding clauses,        wherein the cells of the labeled cell suspension sample are        fixed.        35. The method according to any of the preceding clauses,        wherein the method further comprises fixing the cells of the        neoplasia sample.        36. The method according to Clause 35, wherein fixing the cells        of the neoplasia sample is performed prior to the contacting.        37. The method according to Clause 35, wherein fixing the cells        of the neoplasia sample is performed during the contacting.        38. The method according to Clause 35, wherein fixing the cells        of the neoplasia sample is performed after the contacting.        39. The method according to any of Clauses 35 to 38, wherein        fixing the cells comprises contacting the cells of the neoplasia        sample with a mildly crosslinking agent.        40. The method according to Clause 39, wherein the mildly        crosslinking agent comprises a formaldehyde-based fixative.        41. The method according to any of the preceding clauses,        wherein the predetermined threshold is 100 or more PD-L1        molecules per cell.        42. The method according to clause 41, wherein the predetermined        threshold is 500 or more PD-L1 molecules per cell.        43. The method according to clause 42, wherein the predetermined        threshold is 1000 or more PD-L1 molecules.        44. A method of identifying whether a neoplasia in a subject is        anti-programmed-death ligand 1 (PD-L1) immunotherapy responsive,        the method comprising:    -   contacting a cell suspension sample prepared from the neoplasia        with a labeled binding member specific for PD-L1 to generate a        labeled cell suspension;    -   cytometrically assaying the labeled cell suspension to detect        whether a population of cells that each express a level of PD-L1        that exceeds a predetermined threshold is present to identify        whether the neoplasia is anti-PD-1/PD-L1 immunotherapy        responsive.        45. The method according to Clause 44, wherein the        cytometrically assaying further comprises assaying cell cycle.        46. The method according to Clause 45, wherein assaying cell        cycle comprises quantifying per cell DNA content.        47. The method according to Clause 45 or 46, wherein assaying        cell cycle comprises detecting an expressed cell cycle marker.        48. The method according to any of Clauses 44 to 47, wherein the        method further comprises contacting the cell suspension sample        with a DNA labeling reagent.        49. The method according to any of Clauses 44 to 48, wherein the        method further comprises contacting the cell suspension sample        with a labeled binding member specific for an expressed cell        cycle marker.        50. The method according to any of Clauses 44 to 49, wherein the        cytometrically assaying further comprises assaying aneuploidy.        51. The method according to any of Clauses 44 to 50, wherein the        population of cells is proliferative.        52. The method according to any of Clauses 44 to 51, wherein the        population of cells is aneuploid.        53. The method according to Clause 52, wherein the aneuploid        cells indicate the presence of circulating tumor cells in the        subject.        54. The method according to any of Clauses 44 to 53, wherein the        labeling further comprises contacting the cell suspension sample        with at least one labeled binding member specific for immune        cells.        55. The method according to Clause 54, wherein the at least one        labeled binding member specific for immune cells comprises a        labeled binding member specific for lymphocyte marker CD45.        56. The method according to Clause 54 or 55, wherein the at        least one labeled binding member specific for immune cells        comprises a labeled binding member specific for lymphocyte        marker CD8.        57. The method according to any of Clauses 54 to 56, wherein the        method further comprises cytometrically assaying the labeled        cell suspension to detect whether proliferative immune cells are        present.        58. The method according to Clause 57, wherein the method        further comprises quantifying the amount of proliferative immune        cells.        59. The method according to any of Clauses 54 to 58, wherein        method comprises identifying whether the population of cells is        negative for a marker of immune cells.        60. The method according to any of Clauses 44 to 59, wherein the        population of cells comprises circulating tumor cells.        61. The method according to any of Clauses 44 to 60, wherein the        neoplasia is a hematopoietic cancer.        62. The method according to any of Clauses 44 to 60, wherein the        neoplasia is a solid tumor.        63. The method according to Clause 62, wherein the solid tumor        is an epithelial tumor.        64. The method according to Clause 62 or 61, wherein the solid        tumor is a lung cancer tumor.        65. The method according to Clause 64, wherein the lung cancer        tumor is a non-small cell lung cancer (NSCLC) tumor.        66. The method according to Clause 62 or 63, wherein the solid        tumor is a breast cancer tumor.        67. The method according to any of Clauses 63 to 66, wherein the        population of cells comprises squamous cell carcinoma cells.        68. The method according to any of Clauses 63 to 66, wherein the        population of cells comprises adenocarcinoma cells.        69. The method according to any of Clauses 63 to 66, wherein the        population of cells comprises adenosquamous carcinoma cells.        70. The method according to any of Clauses 44 to 69, wherein the        cell suspension sample is prepared from a biopsy.        71. The method according to Clause 70, wherein the biopsy is a        solid tissue biopsy.        72. The method according to Clause 71, wherein the method        further comprises preparing the cell suspension sample from the        solid tissue biopsy.        73. The method according to Clause 72, wherein preparing the        cell suspension sample from the solid tissue biopsy comprises        homogenizing tissue of the solid tissue biopsy.        74. The method according to Clause 70, wherein the biopsy is a        liquid biopsy.        75. The method according to Clause 74, wherein the method        further comprises preparing the cell suspension sample from the        liquid biopsy.        76. The method according to Clause 70, wherein the biopsy is a        fine needle aspiration (FNA) biopsy.        77. The method according to Clause 76, wherein the method        further comprises preparing the cell suspension sample from the        FNA biopsy.        78. The method according to any of Clauses 44 to 77, wherein the        cells of the labeled cell suspension sample are fixed.        79. The method according to any of Clauses 44 to 78, wherein the        method further comprises fixing the cells of the cell suspension        sample.        80. The method according to Clause 79, wherein fixing the cells        of the cell suspension is performed prior to the contacting.        81. The method according to Clause 79, wherein fixing the cells        of the cell suspension is performed during the contacting.        82. The method according to Clause 79, wherein fixing the cells        of the cell suspension is performed after the contacting.        83. The method according to any of Clauses 79 to 82, wherein        fixing the cells comprises contacting the cells of the cell        suspension sample with a mildly crosslinking agent.        84. The method according to Clause 83, wherein the mildly        crosslinking agent comprises a formaldehyde-based fixative.        85. The method according to any of Clauses 44 to 84, wherein the        predetermined threshold is 100 or more PD-L1 molecules per cell.        86. The method according to clause 85, wherein the predetermined        threshold is 500 or more PD-L1 molecules per cell.        87. The method according to clause 86, wherein the predetermined        threshold is 1000 or more PD-L1 molecules.        88. The method according to any of Clauses 44 to 87, wherein the        cytometrically assaying further comprises quantifying the size        of the population of cells.        89. The method according to Clause 88, wherein if the size of        the population of cells exceeds 1% of the neoplastic cells in        the cell suspension sample the neoplasia is identified as        anti-PD-1/PD-L1 immunotherapy responsive.        90. The method according to any of Clauses 44 to 89, wherein the        neoplasia has been previously identified as PD-L1 positive by        immunohistochemistry.        91. A method of treating a subject for a neoplasia, the method        comprising:    -   administering an anti-PD-1/PD-L1 immunotherapy to a subject        comprising an anti-PD-1/PD-L1 immunotherapy responsive        neoplasia, wherein the neoplasia is identified as        anti-PD-1/PD-L1 immunotherapy responsive according to the method        of any of Clauses 44 to 90.        92. The method according to Clause 91, wherein the subject has        been previously treated with chemotherapy.        93. The method according to Clause 91 or 92, wherein the subject        has been previously treated with radiation therapy.        94. The method according to any of Clauses 91 to 93, wherein the        subject has been previously treated with immunotherapy.        95. The method according to any of Clauses 91 to 94, wherein the        subject has an immune-related disorder or is at increased risk        of developing an immune-related disorder.        96. The method according to any of Clauses 91 to 95, wherein the        anti-PD-1/PD-L1 immunotherapy comprises administering to the        subject one or more anti-PD-1/PD-L1 therapeutic antagonists        selected from the group consisting of: OPDIVO® (nivolumab),        KEYTRUDA® (pembrolizumab), Tecentriq™ (atezolizumab), durvalumab        (MED14736), avelumab (MSB0010718C), BMS-936559 (MDX-1105),        CA-170, BMS-202, BMS-8, BMS-37 and BMS-242.        97. The method according to any of Clauses 91 to 96, wherein the        method further comprises monitoring the anti-PD-1/PD-L1        immunotherapy responsiveness of the neoplasia during the therapy        and continuing the therapy only when the neoplasia is identified        as anti-PD-1/PD-L1 immunotherapy responsive.        98. The method according to Clause 97, wherein the monitoring        comprises:    -   contacting a cell suspension sample from the neoplasia with a        labeled binding member specific for PD-L1 to generate a labeled        cell suspension;    -   cytometrically assaying the labeled cell suspension to detect        whether a population of cells that each express a level of PD-L1        that exceeds a predetermined threshold is present to identify        whether the tumor is anti-PD-1/PD-L1 immunotherapy responsive.        99. A kit comprising:    -   a labeled binding member specific for PD-L1; and    -   a cell suspension fixation solution comprising a fixation        reagent.        100. The kit according to Clause 99, wherein the fixation        reagent is a mildly crosslinking agent.        101. The kit according to Clause 100, wherein the mildly        crosslinking agent comprises a formaldehyde-based fixative.        102. The kit according to any of Clauses 99 to 101, further        comprising a permeabilization reagent.        103. The kit according to Clause 102, wherein the cell        suspension fixation solution comprises the permeabilization        reagent.        104. The kit according to any of Clauses 99 to 103, further        comprising a homogenization device.        105. The kit according to any of Clauses 99 to 104, further        comprising a DNA labeling reagent.        106. The kit according to any of Clauses 99 to 105, further        comprising a labeled binding member specific for an expressed        cell cycle marker.        107. The kit according to any of Clauses 99 to 106, further        comprising at least one labeled binding member specific for        immune cells.        108. The kit according to Clause 107, wherein the at least one        labeled binding member specific for immune cells comprises a        labeled binding member specific for lymphocyte marker CD45.        109. The kit according to Clause 107 or 108, wherein the at        least one labeled binding member specific for immune cells        comprises a labeled binding member specific for lymphocyte        marker CD8.        110. The kit according to any of Clauses 99 to 109, wherein the        kit further comprises a biopsy collection device.        111. A method of detecting whether a neoplastic cell having a        heterogeneity index above a predetermined threshold is present        in a neoplasia sample, the method comprising:    -   contacting the neoplasia sample with a labeled binding member        specific for programmed death ligand (PD-L1) to generate a        labeled cell suspension;    -   cytometrically assaying the labeled cell suspension to obtain a        per cell heterogeneity index comprising quantification of per        cell PD-L1 expression to detect whether a neoplastic cell that        has a heterogeneity index above a predetermined threshold is        present in the neoplasia sample.        112. The method according to Clause 111, wherein the        heterogeneity index comprises a cytometric measurement of cell        complexity.        113. The method according to Clauses 111 or 112, wherein the        heterogeneity index comprises a DNA content determination.        114. The method according to any of Clauses 111 to 113, wherein        the detected cell is proliferative.        115. The method according to any of Clauses 111 to 114, wherein        the labeling further comprises contacting the neoplasia sample        with at least one labeled binding member specific for immune        cells.        116. The method according to any of Clauses 111 to 115, wherein        the detected cell is a circulating tumor cell, a hematopoietic        cancer cell, or a cell of a solid tumor.        117. The method according to any of Clauses 111 to 116, wherein        the predetermined threshold comprises a cell complexity        threshold, a DNA content threshold, and a PD-L1 threshold of 100        or more PD-L1 molecules per cell.        118. A method of indirectly detecting whether circulating tumor        cells (CTCs) are present in a subject having a neoplasia, the        method comprising:    -   contacting a cell suspension sample prepared from the neoplasia        with a DNA labeling reagent or a cell cycle marker to generate a        labeled cell suspension;    -   cytometrically assaying the labeled cell suspension to quantify        whether proliferation in a population of cells of the neoplasia        is above a predetermined threshold to indirectly detect whether        CTCs are present in the subject.        119. The method according to Clause 118, wherein the method        further comprises assessing aneuploidy of the cells of the        population.        120. The method according to Clauses 118 or 119, further        comprising contacting the cell suspension sample with a labeled        binding member specific for PD-L1 and cytometrically assaying        the labeled cell suspension to quantify whether cells of the        population express a level of PD-L1 that exceeds a predetermined        threshold.        121. The method according to any of Clauses 118 to 120, wherein        the neoplasia is a lung cancer.        122. The method according to any of Clauses 118 to 121, wherein        the method further comprises confirming whether CTCs are present        by performing an assay that directly detects CTCs.        123. A method of treating a subject for a neoplasia, the method        comprising:    -   indirectly detecting whether CTCs are present in the subject        according to the method of any of Clauses 118 to 122; and    -   administering to the subject a systemic treatment when CTCs are        indirectly detected to be present and administering to the        subject a local treatment for the neoplasia when CTCs are        absent.        124. The method according to Clause 123, wherein the systemic        treatment comprises radiation therapy, chemotherapy,        immunotherapy, or a combination thereof.        125. A kit comprising:    -   a DNA labeling reagent, a cell cycle marker, a labeled binding        member specific for PD-L1, or a combination thereof;    -   a cell suspension fixation solution comprising a fixation        reagent; and

instructions for performing a method according to any of Clauses 1 to14.

Experimental

The following examples are put forth so as to provide those of ordinaryskill in the art with a complete disclosure and description of how tomake and use the present invention, and are not intended to limit thescope of what the inventors regard as their invention nor are theyintended to represent that the experiments below are all or the onlyexperiments performed. Efforts have been made to ensure accuracy withrespect to numbers used (e.g. amounts, temperature, etc.) but someexperimental errors and deviations should be accounted for. Unlessindicated otherwise, parts are parts by weight, molecular weight isweight average molecular weight, temperature is in degrees Centigrade,and pressure is at or near atmospheric.

General methods in molecular and cellular biochemistry can be found insuch standard textbooks as Molecular Cloning: A Laboratory Manual, 3rdEd. (Sambrook et al., HaRBor Laboratory Press 2001); Short Protocols inMolecular Biology, 4th Ed. (Ausubel et al. eds., John Wiley & Sons1999); Protein Methods (Bollag et al., John Wiley & Sons 1996); NonviralVectors for Gene Therapy (Wagner et al. eds., Academic Press 1999);Viral Vectors (Kaplift & Loewy eds., Academic Press 1995); ImmunologyMethods Manual (I. Lefkovits ed., Academic Press 1997); and Cell andTissue Culture: Laboratory Procedures in Biotechnology (Doyle &Griffiths, John Wiley & Sons 1998), the disclosures of which areincorporated herein by reference. Reagents, cloning vectors, and kitsfor genetic manipulation referred to in this disclosure are availablefrom commercial vendors such as BioRad, Stratagene, Invitrogen,Sigma-Aldrich, and ClonTech.

EXAMPLE 1

Cell suspensions were prepared from freshly collected lung tissue orsamples collected by Fine Needle Aspiration (FNA) according to the FineNeedle non-aspiration cytology (FNNAC) method (a.k.a. “Cytopuncture”method) as described in Brifford et al. (Acta Cytol. 1982 March-April;26 (2):195-200). Samples were collected from subjects with healthy lungsas well as from patients with non-small cell lung cancer (NSCLC).

The freshly collected samples were prepared using the IncellDx, Inc.incellPREP Sample Preparation protocol (IncellDx, Inc. Menlo Park,Calif.). Briefly, the incellPrep protocol is designed to prepare singlecell suspensions from fresh human sourced tissue samples. A homogenizergently disrupts the tissue and the incellPrep reagent fixes andpermeabilizes the individual cells in suspension. The incellPrepprotocol is non-enzymatic. A small sample of the obtained tissue wasplaced in the provided 2 mL microcentrifuge tube with integrated cap.Dulbecco's Phosphate-Buffered Saline, pH 7.4 (D-PBS) (about 800 μL) andthe homogenizer were added to the tube. The homogenizer was connected tothe Power Supply and set to spin the blades at low speed (voltageadjusted to about 1V). Gentle tissue disruption occurred, dislodging theintact cells without shearing the cell membranes. After tissuedisruption was complete, the homogenizer was discarded. The producedcell suspension was centrifuged (at about 600 g for 5 min.) tofacilitate removal of the D-PBS by aspiration. The centrifuged cellswere resuspended in the incellPrep reagent (about 2 mL) for fixation andpermeabilization at ambient temperature for at least 1 hour.

The cell suspensions, either FNNAC or incellPrep prepared, werecentrifuged (600 g for 5 min.), aspirated and a PBS/2% bovine serumalbumin (BSA) solution was added. The PBS/2% BSA solution was removed bycentrifugation and aspiration. The cell suspensions were labeled with anantibody panel containing antibodies for the detection of immune cells(CD3/CD8/CD45) and anti-PD-L1 antibody (Clone 28-8 or E1L3N; fluorescentconjugated) for 30 min. at ambient temperature. The labeling mix wasremoved by centrifugation and aspiration and the cells were washed with1 mL PBS/2% BSA solution with gentle vortexing. Following removal of thewash solution, 200 μL of DAPI labeling solution at working concentrationwas added and the labeled cell suspensions were incubated in the dark,at ambient temperature, for 30 min.

A Beckman Coulter CytoFLEX platform having a 488 nm and 405 nm laserconfiguration was used for cytometric analysis. Control samples (SUPM2,PD-L1 positive control cells; PC3 PD-L1 negative control cells) wereanalyzed for PD-L1 expression. The results of control sample cytometricanalysis, provided in FIG. 1 (left panel—positive control; rightpanel—negative control), showed clear separation between PD-L1expressing and PD-L1 non-expressing cells.

Linearity of flow cytometric quantification of percent PD-L1 positivecells was evaluated. Briefly, cell mixing experiments were performedusing samples of negative cells spiked with a known amount of positivecontrol cells and the samples were assayed for flow cytometric detectionof the positive cells using various anti-PD-L1 antibodies. Data fromlinearity testing is provided in FIG. 2, showing strong linearity forthe calculated PD-L1 positive percentage (y-axis) across mixed cellsamples having various percentages of PD-L1 positive control cells(x-axis).

Linearity of flow cytometric quantification of per cell PD-L1 expressionwas also assayed. Calculated per cell PD-L1 receptor expression wasbased on mean fluorescence intensity of the cell staining using ananti-PD-L1 antibody clone with a known fluorescence to protein (FTP)ratio. Corresponding standard Molecules of Equivalent SolubleFluorochrome (MESF) beads were run with each sample to facilitatequantification. The use of MESF beads, which have known copies of afluorochrome, allows for the derivation of a quantitative standard curvebased on total fluorescence of a bead or cell versus the number offluorescence copies in the known standard. Receptor copy numbers weredetermined on a per cell basis by running the MESF bead standards withevery run and calculating, based on the known number of fluorescencemolecules bound to the antibody (FTP), the receptor copies per cell/celltype. An example of MESF-based standardized quantification is presentedin FIG. 3.

Using a semi-automated, 96-well panel containing the 28-8 anti-PD-L1clone labeled as a 1:1 FTP with Alexa Fluor 647, PD-L1 flow cytometricquantitative assays were validated using patient derived NSCLC samples.Assays included the quantification of the percentage of cell expressingPD-L1 over background as well as the number of PD-L1 receptors on a percell basis. Such quantification was performed for both tumor cells andimmune cell subsets from healthy (“normal lung”) and NSCLC (“Tumor”)patient samples. As shown in FIG. 4, detection of PD-L1 tumor cells waslimited to tumor samples, validating use of this approach to detectPD-L1 positive cells cytometrically.

Testing has shown that PD-L1 expression can be similarly quantified indiploid cells as well as aneuploid cells. Using this approach variousquantitative measures may be assessed including e.g., the percentage oftumor cells expressing PD-L1, the average number PD-L1 receptorsexpressed per tumor cell, the percentage of immune cells expressingPD-L1, the average number PD-L1 receptors expressed per immune cell, thepercent aneuploid tumor cell population expressing PD-L1, the percentdiploid tumor cell population expressing PD-L1, the percent tumorinfiltrating lymphocytes (TIL), etc.

EXAMPLE 2

Further clinical lung samples were prepared and flow cytometricallyanalyzed to obtain PD-L1 and cell cycle dye data for tumor and immunecells. Examples of the data obtained are shown in Table 2, provided inFIG. 5. Also provided for comparison in Table 2 is the percent PD-L1+tumor data as assessed by immunohistochemistry (IHC).

To determine the correlation between single cell PD-L1 quantificationdone non-subjectively using flow cytometry vs. highly subjectiveconventional immunohistochemistry, matched/split samples were analyzedwith one tissue sample submitted for formalin fixed paraffin embeddedslides and another contiguous sample processed through an IVD, enzymefree, single cell preparation device as previously described (Chargin etal., (2016) Cancer Immunol Immunother. 65:1317-23; the disclosure ofwhich is incorporated herein by reference in its entirety).Multi-parameter flow cytometry was performed and single nucleated cellswere gated using PB450-Area vs PB450-Height dot plot analysis. Singlenucleated cells were electronically separated into immune (CD45+, CD3+,CD4+, CD8+) populations and CD45−, diploid and aneuploid tumor cellpopulations. PD-L1 was quantified in the tumor cell and aneuploid tumorcell populations. PD-L1 quantification on the tumor cell population wascompared to IHC quantification. Comparison of the OncoTect iO Lung Assaywith the Dako PD-L1 IHC 28-8 PharmDx Kit revealed an overall concordanceof 95% (diagnostic cutoff: ≥5%; negative percent agreement: 97%;positive percent agreement: 89%; overall agreement: 95%), with detectionof one positive result by the OncoTect iO Lung Assay that was missed byIHC.

Data obtained from 22 clinical lung samples, along with control dataused as baseline, was further analyzed. As the herein described approachquantifies tumor infiltrating lymphocytes (TIL) and cell cycle dye data,the proliferation state of the TILs can be assessed. FIG. 6 shows thepost-G1 amounts of TILs and helper T cells as determined from normaltissue samples, tumor tissue samples (from two independent assays), andcontrol cell samples. This data shows increased proliferation of theTILs present in tumor tissue as compared to those present in normaltissue. In addition, when control PBMCs are used as a marker of PBMCs,the tumor tissues were seen to have an influx of CD8+ TILs (35.9% vs.22.3%). Taken together, this data demonstrates an increase in TILswithin the tumor tissue space and that those TILs have increasedproliferation as compared to normal tissue.

The relative presence of macrophages as compared to non-T cells was alsocompared in the obtained data. As shown in FIG. 7, reduced numbers ofmacrophages were observed in lung tumor tissue samples (two independentassays) as compared to normal lung tissue samples. Thus, the analysismethod described herein also demonstrates that tumor tissues loseantigen presenting cells, as compared to normal tissue. Accordingly,altogether the data presented in this example shows that the describedmethod can detect a loss of macrophages, a gain of non-T cells and anincrease in proliferation of CD8+ TILs and both CD3+ subsets in tumortissue. In addition, as shown in FIG. 8, the described method can alsodetect an increase in aneuploidy among cytotoxic T lymphocytes (CTL), ascompared to the amount of diploid CTLs, in the lung tissue samples(normalized for CTLs in normal tissue).

These data further demonstrate the ability of the herein describedmethods to detect and quantify clinically useful characteristics oftumor tissue samples, including characteristics of immune cells presentin tumor tissues, such as e.g., the size of certain immune cellpopulations within the tumor tissue, the amount of aneuploidy within thepopulations, and the like. Not only can the assay quantify these cellpopulations in the tumor tissue, and ratios thereof, but the use of cellcycle dye analysis further allows one to determine the functional stateof the cells detected, including e.g., the proliferation of immuneinfiltrates.

EXAMPLE 3

As summarized above, the methods described herein can be furtheremployed to, directly or indirectly, analyze tissue samples forcirculating tumor cells (CTC). As an example, lung tissue samples wereflow cytometrically analyzed for immune cell markers, PD-L1 and cellcycle parameters using a cell cycle dye as well as CTC detection. Table3, as follows, provides the data from such assessment.

TABLE 3 Sam- PD- PD- CTC ple CD3 CD8 L1(T) % L1(A) % Aneuploid # PD-L1 184.7 35.2 22.5 28.0 Yes 243 Yes 2 85.7 58.4 0.6 0.6 Yes 9 Yes 3 80.628.85 14.5 No 0 4 79.5 43.5 40.1 50.1 Yes 12 Yes

As can be seen in the above data, the detection of aneuploidy in theprimary lung tumor is indicative of the presence of CTCs. Accordingly,the results presented in this example further support the use ofaneuploidy data, obtained according to the herein described methods froma tumor tissue sample, for predicting whether CTCs are likely to bepresent

EXAMPLE 4

The relationship between differences in PD-L1 expression relative to DNAcontent were further evaluated by comparing quantified PD-L1 expressionas a function of DNA content (FIG. 9). As demonstrated in FIG. 9, DNAcontent as measured by fluorescence intensity typically appears as 1chromosome equivalent (1C) with a small population of cells just priorto cell division appearing as twice (2C) the fluorescence intensity ofdiploid cells (10). Tumor cells that are aneuploid have a DNA contentthat does not fall into the 1C or the 2C fluorescence equivalents. PD-L1expression was found to vary in cells in different phases of the cellcycle, depending on the patient. In particular, the expression of PD-L1was increased in the aneuploid populations relative to the diploidpopulations (FIG. 9).

Tumor heterogeneity was also further addressed. In particular, theinfluence of tumor heterogeneity on factors that influence treatmentsuch as PD-L1 expression, tumor heterogeneity was determined based onthree parameters: PD-L1 expression, side scatter (complexity), and DNAcontent. Based on these three parameters, it was demonstrated thatmultiple different clones of tumor exist in patient samples. When weplotted PD-L1 expression as a function of the determined heterogeneityindex, it was found that the increase in PD-L1 expression is correlatedwith increasing tumor heterogeneity (FIG. 10).

Heterogeneity in NSCLC, both within tumor cells and in the tumormicroenvironment, leads to challenges in tailoring effective patienttreatment strategies. Most conventional molecular-based precisionmedicine diagnostics extract nucleic acids from these heterogeneoustumors and lose the context from which markers are expressed. Diagnosticapproaches such those presented herein can address issues with tumorheterogeneity and the microenvironment by characterizing both the tumorand the tumor microenvironment using a cell-based, multi-parameter assayplatforms. As a clinical assay, such analysis can contribute actionableinformation by quantifying TILs, determining tumor cell aneuploidy, andquantifying PD-L1 on both tumor cells and non-tumor cells in differentphases of the cell cycle.

Anti-tumor immune responses are mediated by CD8+ cytotoxic T-lymphocytes(CTL) and the widespread success of immune checkpoint blockade throughPD-1 and CTLA-4 provides clinical evidence that CTLs are capable ofeffective anti-tumor activity. Tumor infiltrating lymphocytes (TILs)have been shown to be key prognostic determinants in a number of solidtumors. TIL quantification has been included in the panel presentedhere, allowing for predictions of subject survival to be inferred fromintratumor TIL measurements. Using this approach, increases in CD8+ CTLin NSCLC compared to normal lung tissue controls was found. Inparticular, CTLs were significantly increased in aneuploid NSCLC tumorscompared to diploid tumors. Although markers of T-cell exhaustion suchas TIM-3 and CTLA-4 were not included in the current panel,proliferation as determined by post G₀-G₁% in the current study servesas a powerful marker of T-cell activation and activity. Further probingof these CTL infiltrates revealed that the proliferation of theselymphocytes as measured by the post G₀-G₁% demonstrated a decrease inproliferation in the aneuploidy tumors relative to the diploid tumors.Another finding in the current study that may diminish immune controlwas the statistically significant decrease in antigen presenting cellsin NSCLC tissue compared to normal lung tissue.

Aneuploidy, which is found in 65% of NSCLC tumors, is a prognosticfactor in NSCLC. Meta-analyses have concluded that patients with diploidtumors experienced a significant reduction of risk of death from 1 to 5years. Similarly, in other studies, the 3-year survival rate in patientswith aneuploid type tumors was significantly lower than in those withthe diploid type tumors. These studies concluded that the mortality ratein patients with aneuploid tumors was the result of distant metastaseswhile, in patients with diploid tumors, local recurrence was the mainreason for death. In the first three years after surgical resection,patients with aneuploid tumors were found to be at a higher risk ofdistant metastases than patients with the diploid type. Here, we haveshown that 80% of NSCLC was aneuploid with DNA indices greater than1.10. Furthermore, PD-L1 expression was variable from patient to patientdepending on where the tumor cells were in the cell cycle. PD-L1expression in aneuploidy tumor cells is particularly important becauseof the propensity of aneuploidy cells to appear as CTCs and toeventually metastasize.

The relationship between the presence of CTCs, as a surrogate for tumormetastasis, and tumor proliferation was further evaluated. CTCs weredetected using an independent assay and CTC counts were plotted as afunction of tumor proliferation (i.e., post G₀-G₁ in the primary tumor)(FIG. 11). Linear regression of these data revealed a correlationbetween tumor proliferation and the prevalence of CTCs. Accordingly, inthe absence of independent CTC analysis, assaying primary tumorproliferation, as presented in the above described assays, allows forthe presence of CTCs in the blood and, correspondingly, metastases to bepredicted cytometrically.

In addition, the relationship between the presence of CTCs and tumoraneuploidy was also further investigated. Similar to the above, CTCswere detected using an independent assay and CTC counts were measured asa function of tumor cell aneuploidy determined from DNA contentquantification. The result of this analysis is provided in FIG. 12,which shows the mean number of CTCs measured in diploid and aneuploidcell populations. As FIG. 12 depicts, on average, more CTCs are presentin samples with aneuploid cell populations as compared to samples withdiploid cell populations. Accordingly, ploidy status measuredcytometrically in the assays described above also provides a predictiveindicator as to the presence and prevalence of CTCs in a subject.

Overall, the tumor tissue workflow used in the present study resulted inmore actionable information than conventionally used IHC methods. Forexample, it was found that the overall agreement between Oncotect iO andIHC was 95% (supra). In addition, Oncotect iO detected a distinctpopulation of PD-L1 positive cells that was missed by IHC. No cases thatwere positive by IHC were missed by the OncoTect iO Assay. Furthermore,the prognostic information that the OncoTect iO Lung assay provided onTILs and aneuploidy, in addition to PD-L1 expression, positioned thisassay to better inform clinicians about the patient tumor environmentallowing for improved treatment decisions.

Materials and Methods Samples

Fresh tissues were obtained from 19 NSCLC cases. Date of collection,age, sex, ethnicity, diagnosis, primary tumor size, and American JointCommittee on Cancer (AJCC) classification were recorded. Tissues wereexcised and then stored in Roswell Park Memorial Institute (RPMI) 1640medium at 2-8° C. prior to overnight shipment to IncellDx on cold packs.

Tissue Dissociation Using IncellPREP

Tumor biopsies of at least 100 mg were placed in RPMI for transportafter which 4 mm punches were taken from each tissue, of the entiretissue, and placed into Eppendorf tubes containing 800 μL Dulbecco'sphosphate-buffered saline (DPBS). The entire tissue was utilized togenerate the most representative single cell pool of cells to accountfor tumor heterogeneity across the tissue. IncellPREP (IncellDx, Inc)tissue homogenizers were inserted into each tube and set to run untilsupernatant appeared cloudy (<7.5 minutes). Cells were pelleted bycentrifugation at 600×g and fixed and permeabilized in 1 mL IncellMaxper 1 million live cells by trypan blue staining.

OncoTect iO Assay

Aliquots of 250,000 viable cells were tested with the OncoTect iO LungAssay which contains antibodies directed against PD-L1 (28-8), CD45,CD3, and CD8, and a cell cycle dye. Following fixation for 1 hour inIncellMax, 250 μL of sample equivalent to 250,000 cells were aliquotedto 12×75 mm tubes and subsequently washed with 1 mL of DPBS+2% BovineSerum Albumin (BSA). Samples were then stained with PD-L1-Alexa Fluor647 (Clone 28-8, Abcam), CD45-FITC, CD3-PE, and CD8-PC5(B3821F4A/SFCI21Thy2D3/UCHT1, Beckman Coulter) conjugated anti-humanantibodies in DPBS+2% BSA and then incubated for 30 minutes at roomtemperature in the dark. Next, 1 mL of DPBS+2% BSA was added to eachtube and incubated at room temperature for 5 minutes, prior tocentrifugation at 600×g for 5 minutes. Supernatant was aspirated, and awash with DPBS+2% BSA was repeated once. Following this wash, 100 μL ofcell cycle dye at 1 μg/mL was added to each sample and incubated at roomtemperature for 30 minutes in the dark.

Flow Cytometry

Cells were first analyzed on a CytoFlex Cytometer (Beckman Coulter)using a PB450-Area by PB450-Height density plot to set a gate onnucleated single cells by the cell cycle dye staining. That gate wasthen applied to a CD45-FITC by side scatter plot to separate CD45+immune cells from CD45− cells (epithelial/tumor cells). Immune cellswere further separated into CD3+ and CD3+/CD8+ populations by a CD8-PC5by CD3-PE scatter plot. A gate was established around the CD8+/CD3+cells (cytotoxic T-cells). Additionally, a PB450-Lin by count plot wasused to gate on the CD45− diploid population. Once those populationswere determined, each was analyzed for PD-L1 expression by forwardscatter. A putative gate was established based on low/normal PD-L1expression and was validated by this 19-sample dataset. PD-L1 expressionabove the normal cut off was recorded for CD45− population. Similarly,the presence of aneuploid cells was determined by calculating the ratioof Cell Cycle signal in the diploid gate for the CD45− and lymphocytepopulations. A ratio of >1.05 (DNA index) is indicative of aneuploidy.When a ratio of >1.05 was determined, PD-L1 expression on the aneuploidCD45− cells was recorded. Tumor cell clones were calculated using SSCpopulations within the CD45 negative gate, DNA Index and +/−PD-L1expression. The resultant product of these parameters is theheterogeneity index.

Immunohistochemistry

Concordance to IHC was tested by obtaining matched/split FFPE sectionsfrom the tissue biopsies. FFPE blocks were sectioned at 5 μm thickness.Slides were deparaffinized in a series of Xylenes and progressivelydiluted alcohols to water. After rinsing with DI water, the slides weretreated with citrate-based antigen retrieval solution that waspre-heated to 65° C. Slides were incubated in the preheated citratebuffer and heated for 20 minutes at 99° C. and cooled down for 20minutes before commencing immunohistochemical (IHC) staining on the Dakoautostainer. Endogenous peroxidase was quenched with KPL solution,followed by protein blocking and rabbit anti-PD-L1 antibody (28-8 clone)incubation for 1 hour at room temperature. Relevant non-specific isotypecontrol was used as negative control. After rinsing the primaryantibodies, the slides were incubated with biotin conjugated secondaryantibody and HRP-enzyme conjugated streptavidin, followed by incubationwith diaminobenzidine (DAB) to visualize the signal. Upon completion ofthe IHC staining, the slides were de-hydrated in a series of alcoholsand xylenes followed by cover-slipping for microscopic evaluation.

EXAMPLE 5

The comparability of data obtained flow cytometrically and data obtainedusing cell cytometry was compared. Samples were prepared essentially asdescribed above and analyzed in parallel using a flow cytometer and acell cytometer. Analysis showed that various flow cytometric parametersutilized in the methods described herein can be obtained cellcytometrically, e.g., using a CTC cell cytometer/sorter. For example,DNA content data and heterogeneity index data obtained flowcytometrically was comparable to DNA content data and heterogeneityindex data obtained cell cytometrically. An example of the comparabilityof this data is provided in FIG. 13, which depicts PD-L1 expressionversus DNA content obtained using a flow cytometer (left) and a CTC cellcytometer (right). Where cell cytometer analysis is substituted for flowcytometric analysis to obtain parameter used in method of the presentdisclosure, in some instances, corresponding cell cytometric measuresmay be substituted for flow cytometric measures. For example, where flowcytometric side scatter is employed as part of a heterogenetic index, acorresponding cell cytometric measure of cell complexity that ismeasurable by a cell cytometer may be substituted. At least in part,this example shows that certain data, such as DNA content data andheterogeneity index data, useful in the described methods obtained flowcytometrically may also be obtained cell cytometrically from automatedimaging cytometer.

The preceding merely illustrates the principles of the invention. Itwill be appreciated that those skilled in the art will be able to devisevarious arrangements which, although not explicitly described or shownherein, embody the principles of the invention and are included withinits spirit and scope. Furthermore, all examples and conditional languagerecited herein are principally intended to aid the reader inunderstanding the principles of the invention and the conceptscontributed by the inventors to furthering the art, and are to beconstrued as being without limitation to such specifically recitedexamples and conditions. Moreover, all statements herein recitingprinciples, aspects, and embodiments of the invention as well asspecific examples thereof, are intended to encompass both structural andfunctional equivalents thereof. Additionally, it is intended that suchequivalents include both currently known equivalents and equivalentsdeveloped in the future, i.e., any elements developed that perform thesame function, regardless of structure. The scope of the presentinvention, therefore, is not intended to be limited to the exemplaryembodiments shown and described herein. Rather, the scope and spirit ofthe present invention is embodied by the appended claims.

That which is claimed is:
 1. A method of detecting whether a neoplasticcell having a heterogeneity index above a predetermined threshold ispresent in a neoplasia sample, the method comprising: contacting theneoplasia sample with a labeled binding member specific for programmeddeath ligand (PD-L1) to generate a labeled cell suspension;cytometrically assaying the labeled cell suspension to obtain a per cellheterogeneity index comprising quantification of per cell PD-L1expression to detect whether a neoplastic cell that has a heterogeneityindex above a predetermined threshold is present in the neoplasiasample.
 2. The method according to claim 1, wherein the heterogeneityindex comprises a cytometric measurement of cell complexity.
 3. Themethod according to claim 1 or 2, wherein the heterogeneity indexcomprises a DNA content determination.
 4. The method according to any ofthe preceding claims, wherein the detected cell is proliferative.
 5. Themethod according to any of the preceding claims, wherein the labelingfurther comprises contacting the neoplasia sample with at least onelabeled binding member specific for immune cells.
 6. The methodaccording to any of the preceding claims, wherein the detected cell is acirculating tumor cell, a hematopoietic cancer cell, or a cell of asolid tumor.
 7. The method according to any of the preceding claims,wherein the predetermined threshold comprises a cell complexitythreshold, a DNA content threshold, and a PD-L1 threshold of 100 or morePD-L1 molecules per cell.
 8. A method of indirectly detecting whethercirculating tumor cells (CTCs) are present in a subject having aneoplasia, the method comprising: contacting a cell suspension sampleprepared from the neoplasia with a DNA labeling reagent or a cell cyclemarker to generate a labeled cell suspension; cytometrically assayingthe labeled cell suspension to quantify whether proliferation in apopulation of cells of the neoplasia is above a predetermined thresholdto indirectly detect whether CTCs are present in the subject.
 9. Themethod according to claim 8, wherein the method further comprisesassessing aneuploidy of the cells of the population.
 10. The methodaccording to claim 8 or 9, further comprising contacting the cellsuspension sample with a labeled binding member specific for PD-L1 andcytometrically assaying the labeled cell suspension to quantify whethercells of the population express a level of PD-L1 that exceeds apredetermined threshold.
 11. The method according to any of claims 8 to10, wherein the neoplasia is a lung cancer.
 12. The method according toany of claims 8 to 11, wherein the method further comprises confirmingwhether CTCs are present by performing an assay that directly detectsCTCs.
 13. A method of treating a subject for a neoplasia, the methodcomprising: indirectly detecting whether CTCs are present in the subjectaccording to the method of any of claims 8 to 11; and administering tothe subject a systemic treatment when CTCs are indirectly detected to bepresent and administering to the subject a local treatment for theneoplasia when CTCs are absent.
 14. The method according to claim 13,wherein the systemic treatment comprises radiation therapy,chemotherapy, immunotherapy, or a combination thereof.
 15. A kitcomprising: a DNA labeling reagent, a cell cycle marker, a labeledbinding member specific for PD-L1, or a combination thereof; a cellsuspension fixation solution comprising a fixation reagent; andinstructions for performing a method according to any of claims 1 to 14.